scPDB - 5a0y entry

Protein Data Bank Entry:

PDB ID : 5a0y

Resolution :1.100 Å

Experimental Method : X-ray

Deposition Date : 2015-04-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Methyl-coenzyme M reductase I subunit alpha	Methyl-coenzyme M reductase I subunit beta
ID:	MCRA_METTM	MCRB_METTM
AC:	P11558	P11560
Organism:	Methanothermobacter marburgensis
Reign:	Archaea
TaxID:	79929
EC Number:	2.8.4.1

Chains:

Chain Name:	Percentage of Residues within binding site
A	47 %
D	16 %
B	26 %
C	11 %

Ligand binding site composition:

B-Factor:	8.710
Number of residues:	20
Including
Standard Amino Acids:	18
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.125	880.875

% Hydrophobic	% Polar
47.51	52.49
According to VolSite

Ligand :

HET Code:	COM
Formula:	C2H5O3S2
Molecular weight:	141.189 g/mol
DrugBank ID:	DB09110
Buried Surface Area:	56.94 %
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

X	Y	Z
26.2927	33.41	-6.14143

Binding mode :

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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

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
O1S	NH1	ARG- 120	3.08	153.18	H-Bond (Protein Donor)	false
O1S	CZ	ARG- 120	3.77	0	Ionic (Protein Cationic)	false
S1	CZ	TYR- 333	3.95	0	Hydrophobic	false
C2	CE1	PHE- 361	3.8	0	Hydrophobic	false
C2	CE2	TYR- 367	3.74	0	Hydrophobic	false
S1	CZ	TYR- 367	3.98	0	Hydrophobic	false
C1	CB	PHE- 443	3.64	0	Hydrophobic	false
C2	CD2	PHE- 443	4.07	0	Hydrophobic	false
O3S	N	TYR- 444	2.81	156.04	H-Bond (Protein Donor)	false