scPDB - 2c3d entry

Protein Data Bank Entry:

PDB ID : 2c3d

Resolution :2.150 Å

Experimental Method : X-ray

Deposition Date : 2005-10-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	2-oxopropyl-CoM reductase, carboxylating
ID:	XECC_XANP2
AC:	Q56839
Organism:	Xanthobacter autotrophicus
Reign:	Bacteria
TaxID:	78245
EC Number:	1.8.1.5

Chains:

Chain Name:	Percentage of Residues within binding site
A	82 %
B	18 %

Ligand binding site composition:

B-Factor:	15.647
Number of residues:	24
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.206	297.000

% Hydrophobic	% Polar
80.68	19.32
According to VolSite

Ligand :

HET Code:	COM
Formula:	C2H5O3S2
Molecular weight:	141.189 g/mol
DrugBank ID:	DB09110
Buried Surface Area:	74.57 %
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
22.909	-5.35686	14.9513

Binding mode :

What is Poseview ?

2D View
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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
O2S	CZ	ARG- 56	3.9	0	Ionic (Protein Cationic)	false
O3S	CZ	ARG- 56	3.38	0	Ionic (Protein Cationic)	false
O2S	NE	ARG- 56	2.98	165.71	H-Bond (Protein Donor)	false
O3S	NE	ARG- 56	3.31	130.05	H-Bond (Protein Donor)	false
O3S	NH2	ARG- 56	2.6	171.84	H-Bond (Protein Donor)	false
C1	CB	CYS- 82	3.81	0	Hydrophobic	false
S1	SG	CYS- 82	3.72	0	Hydrophobic	false
C1	CG	PRO- 83	4.44	0	Hydrophobic	false
S1	CB	PRO- 83	4.11	0	Hydrophobic	false
S1	CG2	VAL- 88	4.13	0	Hydrophobic	false
C2	SD	MET- 140	3.69	0	Hydrophobic	false
C1	CE	MET- 361	4.03	0	Hydrophobic	false
O1S	NE	ARG- 365	3.07	147.65	H-Bond (Protein Donor)	false
O1S	NH2	ARG- 365	3.01	147.96	H-Bond (Protein Donor)	false
O1S	CZ	ARG- 365	3.48	0	Ionic (Protein Cationic)	false
S1	CZ	PHE- 501	3.86	0	Hydrophobic	false