scPDB - 2ez9 entry

Protein Data Bank Entry:

PDB ID : 2ez9

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2005-11-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pyruvate oxidase
ID:	POXB_LACPL
AC:	P37063
Organism:	Lactobacillus plantarum
Reign:	Bacteria
TaxID:	220668
EC Number:	1.2.3.3

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	9.629
Number of residues:	37
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:	FAD
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.566	239.625

% Hydrophobic	% Polar
67.61	32.39
According to VolSite

Ligand :

HET Code:	TDK
Formula:	C15H22N4O11P3S
Molecular weight:	559.342 g/mol
DrugBank ID:	-
Buried Surface Area:	56.18 %
Polar Surface area:	304.71 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	2
Rings:	2
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
78.1635	62.5931	-0.0942353

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
S1	CG1	VAL- 394	4.22	0	Hydrophobic	false
CMB	CG1	VAL- 394	3.78	0	Hydrophobic	false
O1B	N	ASP- 396	2.92	165.62	H-Bond (Protein Donor)	false
N4'	O	ALA- 420	2.85	152.39	H-Bond (Ligand Donor)	false
C7	CE	MET- 422	3.66	0	Hydrophobic	false
C6	SD	MET- 422	3.99	0	Hydrophobic	false
CM4	SD	MET- 422	3.21	0	Hydrophobic	false
C5'	SD	MET- 422	3.74	0	Hydrophobic	false
CM2	CB	MET- 422	4.12	0	Hydrophobic	false
N3'	N	MET- 422	3.31	172	H-Bond (Protein Donor)	false
O1A	N	GLY- 448	2.89	150.59	H-Bond (Protein Donor)	false
O2A	N	GLY- 449	2.83	144.48	H-Bond (Protein Donor)	false
CM2	SD	MET- 452	3.82	0	Hydrophobic	false
O3B	ND2	ASN- 474	2.97	154.19	H-Bond (Protein Donor)	false
C7	CD1	TYR- 477	4.14	0	Hydrophobic	false
C6	CB	TYR- 477	3.84	0	Hydrophobic	false
CM4	CD1	TYR- 477	4.23	0	Hydrophobic	false
O3B	N	GLY- 478	2.81	160.64	H-Bond (Protein Donor)	false
O1B	N	TRP- 479	2.92	148.18	H-Bond (Protein Donor)	false
C6	CB	TRP- 479	4.14	0	Hydrophobic	false
S1	CB	TRP- 479	3.8	0	Hydrophobic	false
C6	CG1	ILE- 480	3.89	0	Hydrophobic	false
S1	CD1	ILE- 480	3.87	0	Hydrophobic	false
CM4	CG1	ILE- 480	3.84	0	Hydrophobic	false
CMA	CD1	ILE- 480	4.39	0	Hydrophobic	false
OM3	OE2	GLU- 483	2.55	167.21	H-Bond (Protein Donor)	false
O3B	MG	MG- 1510	2.13	0	Metal Acceptor	false
O1A	MG	MG- 1510	2.04	0	Metal Acceptor	false
CMB	C7M	FAD- 1612	3.94	0	Hydrophobic	false
O2B	O	HOH- 2104	2.74	136.76	H-Bond (Protein Donor)	false