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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:

4k6r

1.980 Å

X-ray

2013-04-16

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Bifunctional protein GlmU
ID:GLMU_MYCTU
AC:P9WMN3
Organism:Mycobacterium tuberculosis
Reign:Bacteria
TaxID:83332
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:23.361
Number of residues:34
Including
Standard Amino Acids: 30
Non Standard Amino Acids: 4
Water Molecules: 0
Cofactors:
Metals: MG MG MG

Cavity properties

LigandabilityVolume (Å3)
0.3381103.625

% Hydrophobic% Polar
34.2565.75
According to VolSite

Ligand :
4k6r_1 Structure
HET Code: ATP
Formula: C10H12N5O13P3
Molecular weight: 503.149 g/mol
DrugBank ID: DB00171
Buried Surface Area:65.52 %
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
1.8723232.5725-13.0124


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
C2'CBALA- 143.960Hydrophobic
O1BNGLY- 172.89140.37H-Bond
(Protein Donor)
O1GNTHR- 182.74157.91H-Bond
(Protein Donor)
O1GOG1THR- 183.38141.43H-Bond
(Protein Donor)
O2GCZARG- 193.660Ionic
(Protein Cationic)
O2GNEARG- 192.81171.7H-Bond
(Protein Donor)
O2GNARG- 192.96165.93H-Bond
(Protein Donor)
O3BNH2ARG- 193.14149.42H-Bond
(Protein Donor)
O2'NE2GLN- 832.59133.12H-Bond
(Protein Donor)
O4'NGLY- 882.83133.14H-Bond
(Protein Donor)
O2AMG MG- 5021.910Metal Acceptor
O1AMG MG- 5031.90Metal Acceptor