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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:

1e6v

2.700 Å

X-ray

2000-08-23

Molecular Function:
Binding Site :

Uniprot Annotation

Name:Methyl-coenzyme M reductase I subunit alphaMethyl coenzyme M reductase, beta subunit
ID:MCRA_METKAQ49601_9EURY
AC:Q49605Q49601
Organism:Methanopyrus kandleri
Reign:Archaea
TaxID:1901922320
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A44 %
D17 %
B28 %
C11 %


Ligand binding site composition:

B-Factor:20.326
Number of residues:20
Including
Standard Amino Acids: 18
Non Standard Amino Acids: 2
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.028327.375

% Hydrophobic% Polar
43.3056.70
According to VolSite

Ligand :
1e6v_4 Structure
HET Code: COM
Formula: C2H5O3S2
Molecular weight: 141.189 g/mol
DrugBank ID: DB09110
Buried Surface Area:53.94 %
Polar Surface area: 104.38 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 1
Rings: 0
Aromatic rings: 0
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
65.74249.49386109.196


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
C1CZTYR- 3364.430Hydrophobic
S1CE2TYR- 3363.740Hydrophobic
C2CE1PHE- 3624.170Hydrophobic
C2CE1TYR- 3683.870Hydrophobic
S1CZTYR- 3684.210Hydrophobic
C1CBPHE- 4463.670Hydrophobic
O1SNTYR- 4472.89175.68H-Bond
(Protein Donor)