Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

3vqm

2.550 Å

X-ray

2012-03-26

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Small heat shock protein StHsp14.0
ID:Q970D9_SULTO
AC:Q970D9
Organism:Sulfolobus tokodaii
Reign:Archaea
TaxID:273063
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
I95 %
M5 %


Ligand binding site composition:

B-Factor:60.364
Number of residues:19
Including
Standard Amino Acids: 19
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.877273.375

% Hydrophobic% Polar
53.0946.91
According to VolSite

Ligand :
3vqm_6 Structure
HET Code: VAL_ILE_LYS_ILE_GLU
Formula: C28H52N6O8
Molecular weight: 600.748 g/mol
DrugBank ID: -
Buried Surface Area:29.43 %
Polar Surface area: 251.93 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 6
Rings: 0
Aromatic rings: 0
Anionic atoms: 2
Cationic atoms: 2
Rule of Five Violation: 3
Rotatable Bonds: 21

Mass center Coordinates

XYZ
-56.44570.83042914.8486


Binding mode :
What is Poseview ?
  • 2D View
  • 3D View
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
ONZLYS- 473.18152.1H-Bond
(Protein Donor)
OXTNZLYS- 473.670Ionic
(Protein Cationic)
NOALA- 522.88155.14H-Bond
(Ligand Donor)
CD1CBALA- 524.270Hydrophobic
CG2CBARG- 534.10Hydrophobic
CD1CD1LEU- 604.20Hydrophobic
CG2CG2ILE- 994.160Hydrophobic
CD1CG2ILE- 993.620Hydrophobic
NOGLY- 1012.7154.66H-Bond
(Ligand Donor)
CG2CBTYR- 1033.70Hydrophobic
CG2CD1LEU- 1083.950Hydrophobic
CD1CD1LEU- 1084.020Hydrophobic
CD1CD1ILE- 1103.680Hydrophobic