ProCarbDB

An open access database ready to answer your sweetest queries

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Query the database

All the queries are performed using the Query Page. Some queries take more time to be retrieved than others. While the backend is retrieving information from the database the following loading GIF will appear:

The user can query the database using 9 different options:

  1. PDB ID Search

    Entering a PDB ID (Ex.: 2vu9) and hitting the 'Submit' button will redirect the user to the General Information page where a summary for that entry will be available; or if the entry is not present in the database a message will appear.

    Entering a list of PDB IDs separated by a comma (2vu9,3h2k,3nsn...) and hitting the 'Submit button' will redirect the user to the Multiple Results page where all the results will be presented in a table. If no search entries are present in the database a message will appear.
    Information on PDB ID nomenclature can be found here.

  2. Uniprot ID Search

    Entering a Uniprot ID (Ex.: B7XC04), a list of Uniprot IDs separated by comma (Q9X0S8,O00214,Q06GJ0...), keywords(lectin),wildcards to perform searches for partial terms (e.g. lec*). Capitalization is not taken into consideration. Hitting the 'Submit' button will redirect the user to the:

    • General Information page, if only one hit was found in the database (where a summary for that entry will be available)
    • Multiple Results page, if more than one hit was found in the database.
    • A message, if no hits were found in the database
    Information on Uniprot ID nomenclature can be found here.

  3. PFAM ID Search

    Entering a PFAM ID (Ex.: PF00534.19) or a list of PFAM IDs separated by comma (Ex.: PF00534.19,PF13439.5,PF03370.12...), keywords(glucanase), wildcards to perform searches for partial terms (e.g. *ase). Capitalization is not taken into consideration. Hitting the 'Submit' button will redirect the user to the:

    • General Information page, if only one hit was found in the database (where a summary for that entry will be available)
    • Results Page, if more than one hit was found in the database (each hit will display the PDB ID and the PFAM ID).
    • A message, if no hits were found in the database
    Information on Pfam ID nomenclature can be found here.

  4. Enzyme Classification Search

    Entering an EC ID (Ex.: 1.1.1.1) or a list of PFAM IDs separated by comma (Ex.: PF00534.19,PF13439.5,PF03370.12...), keywords(phosphorylase), wildcards to perform searches for partial terms (e.g. *ase). Capitalization is not taken into consideration. Hitting the 'Submit' button will redirect the user to the:

    • General Information page, if only one hit was found in the database (where a summary for that entry will be available)
    • Results Page, if more than one hit was found in the database (each hit will display the PDB ID and the ProCarbDB Ligand ID).
    • A message, if no hits were found in the database
    Information on EC ID nomenclature can be found here.
  5. Sequence Search

    This type of query performs a standard BLAST alignment with expected value (E-value) = 0.001, percentage of identical matches (pident) = 85% and query coverage per subject = 85%. For more information on this parameters click here.

  6. PDB Ligand ID Search

    Entering a Ligand PDB ID (Ex.: MAN) or a list of Ligand PDB IDs separated by comma (Ex.: MAN,GLC,SIA...), keywords(glucose), wildcards to perform searches for partial terms (e.g. gluc) can be used. Hitting the 'Submit' button will redirect the user to the:

    For a complete understanding of the colour coding used for 3D rendering of carbohydrate units please click HERE
    • General Information page, if only one hit was found in the database (where a summary for that entry will be available)
    • Results Page, if more than one hit was found in the database.
    • A message, if no hits were found in the database

    Ligand PDB ID nomenclature can be found here and can be downloaded here.
    NOTE: PDB annotates around 500 Ligands as carbohydrates, while we identified with the help of pdb-care more than 800.

  7. Organism Search

    Entering an organism (Ex.: homo sapiens) or a list of organisms separated by comma (homo sapiens,mus musculus...), keywords(sapiens), wildcards to perform searches for partial terms (e.g. sap*) can be used. Hitting the 'Submit' button will redirect the user to the:

    • General Information page, if only one hit was found in the database (where a summary for that entry will be available)
    • Multiple Results page, if more than one hit was found in the database.
    • A message, if no hits were found in the database
  8. Feature Search

    This type of query will retrieve the common set between selected features.

    • Has affinity value: will retrieve only ProCarbDB entries that have at least one registered biophysical measurement (of any kind).
    • Has mutants: will retrieve only ProCarbDB entries that have at least one mutant.
    • No occupancy issues: will retrieve only ProCarbDB entries that have at least one ligand clearly identified (in the PDB file occupancy is 1 for each atom of a ProCarbDB Ligand).
    • Single binding pocket: will retrieve only ProCarbDB entries that have only one binding pocket PER CHAIN.
  9. Affiny Search

    Using this type of query the user can select the type of biophysical measurement he/she wants to inspect. Possible queries:

    • Dissociation constant (Kd), unit: Molar (M)
    • Association constant (Ka), unit: 1/Molar (1/M)
    • Inhibitory constant (Ki), unit: Molar (M)
    • Half maximal effective concentration (EC50), unit: Molar (M)
    • Half maximal inhibitory concentration (IC50), unit: Molar (M)
    • Gibbs free energy Δ G, unit: Joules (J)
    • Association and Dissociation rates (kon and koff), units: Molar-1×sec-1 and sec-1, respectively.
    • negative log of Kd and negative log of Ki, units: not applicable (N/A)

Multiple Hits Page

Below is the standard output for multiple results:


General Information Page

On this page the user can access information from 3 separate databases: PubMed, Uniprot, Pfam as well as display several features of the 3D crystal structure using the Structure View (we only display the asymmetric unit).


Ligand Information Page

Below you can see how different monomers are encoded with different colours. Sialic Acid is the only comon monomer encoded with the same colour.

Mutant Information Page

View Controls:

  1. General Movement
    • To rotate structure: hold left-click and move mouse in any direction
    • To translate canvas: hold right-click and move mouse in any direction
    • To zoom: use scroll button counter-clockwise to zoom-in and clockwise to zoom out
    • Atom/Bond information: hover over desired atom/bond
    • Distance/Angle/Dihedral measurements. Hold Ctrl and press left-click on 2 atoms(for distance), 3atoms(for angle) or 4 atoms(dihedral). Finally, select again one of the already selected atoms in order to finish the measurements. To remove a measurement select all involved atoms.
  2. Structure View
    • Three representation styles are available:
      • Surface: (opacity needs to be different than 0) the Van der Walls surface representation
      • Cartoon: the main backbone atoms (see backbone) of successive residues in unbroken chains are connected by a smooth trace. The trace is expanded perpendicular to its tangent with an elliptical cross-section. The major axis points from .CA in the direction of the .O in case of proteins
      • Ball and Stick: atoms are displayed as spheres (balls) and bonds as cylinders (sticks).
    • Seven colouring styles are available in total:
      • Hydrophobicity:coloured from red (hydrophilic) to green (hydrophobic).
      • Secondary Structures:
        Alpha Helix
        Beta Strand
        Beta Turn
        Coil
        3/10 Helix
        Pi Helix
      • Residue:
        Ala(A)
        Arg(R)
        Asn(N)
        Asp(E)
        Cys(C)
        Gln(Q)
        Glu(D)
        Gly(G)
        His(H)
        Ile(I)
        Leu(L)
        Lys(K)
        Met(M)
        Phe(F)
        Pro(P)
        Ser(S)
        Thr(T)
        Trp(W)
        Tyr(Y)
        Val(V)
      • B-factor: a factor that can be applied to the X-ray scattering term for each atom (or for groups of atoms) that describes the degree to which the electron density is spread out. While the theory is that the B-factor indicates the true static or dynamic mobility of an atom, it can also indicate where there are errors in model building. Coloured from red (low b-factor) to pale yellow (high b-factor)
      • Pfam: based on the start and end points (displayed in the Domains table). Due to the fact that each structure has a variable number of Pfam domains, all the residues that ARE NOT part of a Pfam domain will be coloured in GREY. Distinct domains will present distinct colours
      • Density Fit: it is a 3D representation of the validation reports (wwPDB Validation Reports ) available for each PDB structure. This colouring is done by overlapping the experimental electron density with the model: blue regions represent a good fit between the two while red regions represent a bad fit between the two.
      • Geometric Quality colours each protein amino acid (by residue) and ligand molecule (by atom) based on the number of geometric issues (see below).
        0
        1
        2
        ≥ 3
        Examples of geometric issues: steric clashes, Ramachandran outliers, sidechain conformation outliers
    • Seven Check boxes are available:
      • Cartoon: default is 'checked' and displays cartoon representation (see representation part)
      • Ball and Stick: default is 'unchecked'. If checked displays ball and stick representation (see representation part)
      • Clashes: default is 'unchecked'. If checked it displays steric clashes (the degree of van der Waals (vdW) spheres overlap between the two atoms) as pink disks (the larger the disk the larger the overlap). Furthermore, the residues of the corresponding atoms are displayed as Ball and Stick representation and coloured by Geometric Quality.
        NOTE: For the best visualization of clashes: color the cartoon representation by chain and 'check' the clashes box
      • Water, Ion and Ligand boxes: if checked they display water, ion and ligand molecules respectively.
        Note: In order to view Ligand Contacts all three boxes need to be checked
      • Ligand Contacts box: if checked, displays all the contacts the ligand makes. Hover over contact lines to check the nature of the interaction.
  3. Ligand View
    Information about representation types and colouring schemes is provided above.
    General movements and measurements apply on this View as explained here.
    The Ligands are coloured in based on a predefied colour scheme where each monomer has a different colour.
    All protein residues that are 4Å or closer to the selected Ligand are coloured in LIGHT GREY.
    All protein residues that further than 4Å to the selected Ligand are coloured in LIGHT GREY. NOTE: These residues are displayed only for the 'For Mutagenesis' option of the 'Choose interaction partners panel'(See more below).

    Once a ligand has been selected the default 'Choose Interaction Partners' is 'Between Ligand and all molecules' which will show all the interaction partners 4Å or closer to the selected ligand. The user has the chance to further inspect the interactions the ligand is making with: i) itself, ii)water molecules and iii)protein residues by selecting the appropriate option from the 'Chose Interaction Partners' panel. 'For Mutagenesis' is a special option in this panel that allows the user to select any residue that is 4Å or closer to the ligand). Once an amino acid is selected, its colour will change to ORANGE and only the interactions that this residue is making with i)the ligand and ii)other amino acid residues will be displayed. This allows the user to better understand the impact of a putative mutation, because he can infer which bonds and interaction will be disrupted upon mutagenesis.

    NOTE: Not all displayed residues will present contacts, they are presented to inform the user about the spatial arrangement of the binding pocket and the impact a mutation might have.

    Ligand view 1
    Ligand view 2 (For Mutagenesis Panel)
    Types of interactions available:
    • Hydrogen Bonds:

      Are calculated as described in:

      DF Stickle, LG Presta, KA Dill, GD Rose.
      (1992) Hydrogen bonding in globular proteins. JMB.doi:10.1016/0022-2836(92)91058-W
      P Zhou, F Tian, F Lv, Z Shang.
      (2008)Geometric characteristics of hydrogen bonds involving sulfur atoms in proteins, Proteins doi:10.1002/prot.22327

      Briefly, hydrogen bonds are calculated between a donor atom (in general all oxygen, nitrogen and sulphur atoms) and an acceptor atom (in general all oxygen atoms, nitrogen atoms with a charge less than 1 and one free electron pair or any nitrogen atom present in the ring of His, and sulphur atoms present in Cys or Met) with a maximum distance of 3.5Å (4.1Å for Sulphur)

    • Weak Hydrogen Bonds:

      Are calculated as deschibred in:

      Taylor R and Kennard O.
      (1982) Crystallographic evidence of the existence of CH.cntdot..cntdot..cntdot.O, CH.cntdot..cntdot..cntdot.N and CH.cntdot..cntdot..cntdot.Cl hydrogen bonds. JACS, https://pubs.acs.org/doi/abs/10.1021/ja00383a012

      Briefly, they are calculated as described in the Hydrogen Bonds section with the mention that the donor atom is a carbon atom.

    • Hydrophobic Interactions:

      Are calculated as described in:

      RF de Freitas and M Schapira.
      (2017)A systematic analysis of atomic protein–ligand interactions in the PDB. Med Chem Commun, doi:10.1039/C7MD00381A

      Briefly, hydrophobic interactions are calculated between carbon atoms that are covalently bound only to carbon or hydrogen atoms with a maximum distance of 4.0Å.

    • Ionic Bond:

      Are calculated as described in https://www.britannica.com/science/crystal/Types-of-bonds#ref51815 and https://www.britannica.com/science/ionic-bond

      Briefly, an ionic bond represents the electrostatic interaction between two ions (one is a metal and the other is a potential metal binding partners) formed through the transfer of one or more electrons and a maximum distance of 5.0Å
      Metal Classes:
      • Alkali & Alkaline earth: Li, Na, K, Rb, Cs, Mg, Ca, Sr, Ba
      • Transition Metals: Groups IIIB-XIIB
      • Other Metals: Al, Ga, In, Tl, Sc, Sn, Pb, Bi, Sb, Hg
      • Actinides & Lanthanides & Y
      Potential Metal Binding Partners:
      • Halogens: F, Cl, Br, I, At, Ts
      • Amino acids: Oxygen in backbone; oxygen in sidechain of: Asp, Glu, Ser, Thr, Tyr, Asn, Gln; Sulfur in Cys.
      • Functional groups of ligands: Oxygen, Sulphur, Halogens
    • Metal Interactions:
      Are calculated as described here.
      Briefly, a metal interaction is defined as a dataive(co-ordinate) bond between metal classes and potential binding partners. Metal Classes:
      • Transition Metals: Groups IIIB-XIIB
      Potential Metal Binding Partners:
      • Halogens: F, Cl, Br, I, At, Ts
      • Amino acids: Oxygen in backbone; oxygen in sidechain of: Asp, Glu, Ser, Thr, Tyr, Asn, Gln; Sulfur in Cys, Nitrogen in sidechain of His
      • Functional groups of ligands: Oxygen, Sulphur, Nitrogen, Halogens
    • Halogen Bonds:

      Are calculated as described in:

      P Auffinger, FA Hays, E Westhof, and PS Ho.
      (2004)Halogen bonds in biological molecules. PNAS,doi:10.1073/pnas.0407607101

      Briefly, halogen bonds are calculated between donors X-C(where X is Cl,Br,I or At and not F ) and acceptors Y-Z(where Y is C, P, N or S, and Y is O, N or S) with a maximum distance of 4.0Å

    • Pi Stacking:
      pi-stacking interactions
      cation-pi interactions

      Are calculated as described in

      JP Gallivan and DA Dougherty.
      (1999)Cation-π interactions in structural biology. PNAS, doi:10.1074/jbc.273.25.15458.

      GB McGaughey, M Gagné and AK Rappé.
      (1998) π-Stacking Interactions - ALIVE AND WELL IN PROTEINS. JBC,doi:10.1074/jbc.273.25.15458.

      Briefly, pi-stacking interactions are parallel or T-shaped stacking of electron clounds involved in ring formation(benzene) with a maximum distance of 5.5Å. Briefly, cation-pi interactions are interactions between postive charged center (Nitrogen sidechain atoms in Arg, His, Lys; atoms in Guanidine, Acetamidine groups; atoms with a positive charge) and electron clounds involved in ring formation(benzene) with a maximum distance of 6Å.

    NOTE: All deffinitions follow the NGL constrains and the RCSB guidlines
  4. Mutant View
    Surface representation is coloured by hydrophobicity by default. More on colouring and representations here. Contacts are provided only for the ligand. More on contact types here. General movements and measurements apply on this View as explained here. The novelty in this view comes from the fact that each mutant present in the Mutant Information is coloured differently and displayed as ball + stick representation (more on this here ). This allows the user to infer if the experimentally validated mutations are in the vecinity of the binding pocket or not. Some structures have many mutations and thus distinguishing each mutated residue is hard. For this reason we offer a 'Mutated Res' panel where the user can select any mutated residue and the interactive window will zoom on selected residue. div style="width: 100%" >