scPDB - 2rgh entry

Protein Data Bank Entry:

PDB ID : 2rgh

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2007-10-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Alpha-Glycerophosphate Oxidase
ID:	D0VWY7_STRSP
AC:	D0VWY7
Organism:	Streptococcus sp
Reign:	Bacteria
TaxID:	1306
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	34.934
Number of residues:	70
Including
Standard Amino Acids:	67
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.646	806.625

% Hydrophobic	% Polar
48.54	51.46
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	79.4 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
25.6248	22.585	64.0279

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
C4'	CG2	ILE- 28	4.19	0	Hydrophobic	false
O1P	N	THR- 29	2.87	161.85	H-Bond (Protein Donor)	false
O2P	OG1	THR- 29	2.73	169.28	H-Bond (Protein Donor)	false
O3B	OE2	GLU- 48	2.53	169.59	H-Bond (Ligand Donor)	false
O3B	OE1	GLU- 48	3.03	124.31	H-Bond (Ligand Donor)	false
O2B	OE1	GLU- 48	2.57	170.17	H-Bond (Ligand Donor)	false
C1B	CG	MET- 49	4.46	0	Hydrophobic	false
N3A	N	MET- 49	3.1	155.45	H-Bond (Protein Donor)	false
O2B	NE2	GLN- 50	2.98	161.1	H-Bond (Protein Donor)	false
O1A	N	THR- 56	2.79	155.97	H-Bond (Protein Donor)	false
C5'	CB	THR- 56	4.3	0	Hydrophobic	false
C3'	CG2	THR- 56	3.81	0	Hydrophobic	false
C9	CG2	THR- 56	3.93	0	Hydrophobic	false
O2A	OG	SER- 57	2.62	154.39	H-Bond (Protein Donor)	false
O2A	N	SER- 57	2.82	143.98	H-Bond (Protein Donor)	false
O4'	OG	SER- 57	2.99	160.28	H-Bond (Ligand Donor)	false
C6	CB	SER- 60	4.27	0	Hydrophobic	false
C9A	CB	SER- 60	3.81	0	Hydrophobic	false
N5	N	THR- 61	3.21	159.7	H-Bond (Protein Donor)	false
N5	OG1	THR- 61	3.43	155.47	H-Bond (Protein Donor)	false
C6	CB	THR- 61	4.5	0	Hydrophobic	false
N3	O	LEU- 63	2.95	144.25	H-Bond (Ligand Donor)	false
N6A	O	ALA- 197	3.05	163.02	H-Bond (Ligand Donor)	false
N1A	N	ALA- 197	2.8	173.91	H-Bond (Protein Donor)	false
C5B	CE3	TRP- 235	4.07	0	Hydrophobic	false
C2B	CZ3	TRP- 235	3.79	0	Hydrophobic	false
C7M	CB	THR- 298	4.47	0	Hydrophobic	false
C8M	CG	ARG- 346	3.4	0	Hydrophobic	false
C8	CG	ARG- 346	3.65	0	Hydrophobic	false
C3'	CG	PRO- 347	4.25	0	Hydrophobic	false
C5'	CG	PRO- 347	4.17	0	Hydrophobic	false
O2	NZ	LYS- 429	3.45	141.69	H-Bond (Protein Donor)	false
N1	N	ILE- 430	3.45	147.27	H-Bond (Protein Donor)	false
C4'	CG1	ILE- 430	3.68	0	Hydrophobic	false
O2	N	THR- 431	2.97	154.81	H-Bond (Protein Donor)	false
O2	OG1	THR- 431	3.33	167.27	H-Bond (Protein Donor)	false
O1P	O	HOH- 734	2.62	179.99	H-Bond (Protein Donor)	false
O2P	O	HOH- 780	2.83	128.94	H-Bond (Protein Donor)	false