scPDB - 2jib entry

Protein Data Bank Entry:

PDB ID : 2jib

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2007-02-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Oxalyl-CoA decarboxylase
ID:	OXC_OXAFO
AC:	P40149
Organism:	Oxalobacter formigenes
Reign:	Bacteria
TaxID:	847
EC Number:	4.1.1.8

Chains:

Chain Name:	Percentage of Residues within binding site
A	71 %
B	29 %

Ligand binding site composition:

B-Factor:	35.465
Number of residues:	54
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	2
Water Molecules:	6
Cofactors:	COA
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.495	259.875

% Hydrophobic	% Polar
55.84	44.16
According to VolSite

Ligand :

HET Code:	TPP
Formula:	C12H16N4O7P2S
Molecular weight:	422.291 g/mol
DrugBank ID:	-
Buried Surface Area:	85.76 %
Polar Surface area:	225.32 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	1
Rings:	2
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
80.6774	-3.91154	0.933077

Binding mode :

What is Poseview ?

2D View
3D View

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
CM4	CG1	VAL- 31	4.06	0	Hydrophobic	false
C5'	CG2	VAL- 79	3.9	0	Hydrophobic	false
CM2	CB	PRO- 82	4.26	0	Hydrophobic	false
O2B	OH	TYR- 377	2.67	123.94	H-Bond (Protein Donor)	false
S1	CB	ALA- 401	4.12	0	Hydrophobic	false
C7	CB	ALA- 401	3.72	0	Hydrophobic	false
O3A	N	ALA- 401	3.12	174.8	H-Bond (Protein Donor)	false
O1B	N	ASN- 402	2.74	150.59	H-Bond (Protein Donor)	false
O1B	ND2	ASN- 402	2.7	169.96	H-Bond (Protein Donor)	false
O2B	N	ALA- 403	3	135.51	H-Bond (Protein Donor)	false
N4'	O	GLY- 426	2.78	152.91	H-Bond (Ligand Donor)	false
C5'	CG	MET- 428	4.17	0	Hydrophobic	false
S1	SD	MET- 428	3.79	0	Hydrophobic	false
CM4	CG	MET- 428	4.16	0	Hydrophobic	false
C6	CG	MET- 428	3.99	0	Hydrophobic	false
O1A	N	SER- 453	3.03	155.01	H-Bond (Protein Donor)	false
C6	CB	SER- 453	3.82	0	Hydrophobic	false
O2A	N	ALA- 454	2.75	155.93	H-Bond (Protein Donor)	false
CM2	CE2	PHE- 457	3.36	0	Hydrophobic	false
CM4	CZ	PHE- 457	4.22	0	Hydrophobic	false
O3B	ND2	ASN- 479	3.3	143.93	H-Bond (Protein Donor)	false
CM4	CD1	ILE- 482	4.34	0	Hydrophobic	false
C7	CG2	ILE- 482	3.49	0	Hydrophobic	false
C7	CE2	TYR- 483	3.91	0	Hydrophobic	false
O3B	N	TYR- 483	3.08	124.93	H-Bond (Protein Donor)	false
O1A	MG	MG- 1567	2.22	0	Metal Acceptor	false
O3B	MG	MG- 1567	2.15	0	Metal Acceptor	false
S1	S1P	COA- 1569	3.4	0	Hydrophobic	false
O2B	O	HOH- 2330	3.1	150.72	H-Bond (Protein Donor)	false