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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

4ymv

3.000 Å

X-ray

2015-03-07

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:ABC-type polar amino acid transport system, ATPase component
ID:Q8RCC2_CALS4
AC:Q8RCC2
Organism:Caldanaerobacter subterraneus subsp. tengcongensis
Reign:Bacteria
TaxID:273068
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A11 %
J89 %


Ligand binding site composition:

B-Factor:70.124
Number of residues:27
Including
Standard Amino Acids: 27
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.1951360.125

% Hydrophobic% Polar
29.2870.72
According to VolSite

Ligand :
4ymv_2 Structure
HET Code: ATP
Formula: C10H12N5O13P3
Molecular weight: 503.149 g/mol
DrugBank ID: DB00171
Buried Surface Area:49.59 %
Polar Surface area: 319.88 Å2
Number of
H-Bond Acceptors: 17
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
-20.72234.372915.6786


Binding mode :
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Binding mode
BioSolveIT Image generated by PoseView
Protein
Binding Site
Ligand
Interaction pattern
hydrophobic (CA)
aromatic (CZ)
hydrogen bond acceptor (O)
hydrogen bond acceptor/donor (OG)
hydrogen bond donor (N)
positively ionized (NZ)
negatively ionized (OD1)
metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
DuArDuArPHE- 113.950Aromatic Face/Face
C5'CG1VAL- 164.50Hydrophobic
O2BOGSER- 363.29125.22H-Bond
(Protein Donor)
O1BNGLY- 373.44120.8H-Bond
(Protein Donor)
O3ANGLY- 372.83171.64H-Bond
(Protein Donor)
O1ANGLY- 392.89150.96H-Bond
(Protein Donor)
O2GNZLYS- 403.890Ionic
(Protein Cationic)
O2BNZLYS- 403.760Ionic
(Protein Cationic)
O1ANZLYS- 403.740Ionic
(Protein Cationic)
O2ANZLYS- 402.540Ionic
(Protein Cationic)
O1ANLYS- 403.49143.19H-Bond
(Protein Donor)
O2ANZLYS- 402.54137.79H-Bond
(Protein Donor)
O3GOGSER- 412.62148.89H-Bond
(Protein Donor)
O5'NSER- 413.12170.86H-Bond
(Protein Donor)
C3'CBSER- 413.930Hydrophobic
O2GNE2HIS- 1943.14139.63H-Bond
(Protein Donor)