scPDB - 1wv4 entry

Protein Data Bank Entry:

PDB ID : 1wv4

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2004-12-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pyridoxine/pyridoxamine 5'-phosphate oxidase
ID:	PDXH_ECOLI
AC:	P0AFI7
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	42 %
B	58 %

Ligand binding site composition:

B-Factor:	51.629
Number of residues:	36
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.109	820.125

% Hydrophobic	% Polar
41.56	58.44
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	64.46 %
Polar Surface area:	217.05 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
50.4979	39.0852	48.5219

Binding mode :

What is Poseview ?

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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
C2'	CG	ARG- 67	4.03	0	Hydrophobic	false
C3'	CB	ARG- 67	4	0	Hydrophobic	false
O1P	NE	ARG- 67	2.82	152.25	H-Bond (Protein Donor)	false
O1P	NH2	ARG- 67	2.96	141.7	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 67	3.32	0	Ionic (Protein Cationic)	false
C7M	CG2	ILE- 68	4.14	0	Hydrophobic	false
C8M	CD1	ILE- 68	4.31	0	Hydrophobic	false
C9	CB	ILE- 68	4.23	0	Hydrophobic	false
C9A	CG2	ILE- 68	4.42	0	Hydrophobic	false
C7	CG2	ILE- 68	3.67	0	Hydrophobic	false
O2'	O	ILE- 68	3.03	145.09	H-Bond (Ligand Donor)	false
O4	N	LEU- 70	3.15	167.54	H-Bond (Protein Donor)	false
C6	CG	LEU- 70	3.74	0	Hydrophobic	false
N3	O	TYR- 82	2.65	177.14	H-Bond (Ligand Donor)	false
O2P	NZ	LYS- 89	3.14	166.16	H-Bond (Protein Donor)	false
O2P	N	LYS- 89	2.82	146.35	H-Bond (Protein Donor)	false
O2P	NZ	LYS- 89	3.14	0	Ionic (Protein Cationic)	false
C7M	CB	HIS- 106	3.76	0	Hydrophobic	false
C8M	CG	GLN- 111	3.74	0	Hydrophobic	false
O2'	NE2	GLN- 111	2.67	156.81	H-Bond (Protein Donor)	false
C8M	CZ3	TRP- 191	3.33	0	Hydrophobic	false
C1'	CZ2	TRP- 191	3.72	0	Hydrophobic	false
C9	CH2	TRP- 191	3.44	0	Hydrophobic	false
O3P	CZ	ARG- 201	3.81	0	Ionic (Protein Cationic)	false
O3P	NH2	ARG- 201	3.22	144.42	H-Bond (Protein Donor)	false