scPDB - 1gpe entry

Protein Data Bank Entry:

PDB ID : 1gpe

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 1999-03-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glucose oxidase
ID:	GOX_PENAG
AC:	P81156
Organism:	Penicillium amagasakiense
Reign:	Eukaryota
TaxID:	63559
EC Number:	1.1.3.4

Chains:

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

Ligand binding site composition:

B-Factor:	8.342
Number of residues:	71
Including
Standard Amino Acids:	66
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.571	401.625

% Hydrophobic	% Polar
64.71	35.29
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	83.17 %
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
3.90413	9.84851	-23.2868

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
O2A	N	LEU- 34	3.14	172.16	H-Bond (Protein Donor)	false
C4'	CD1	LEU- 34	3.94	0	Hydrophobic	false
C5'	CB	LEU- 34	4.49	0	Hydrophobic	false
O1P	N	THR- 35	2.81	171.2	H-Bond (Protein Donor)	false
O1P	OG1	THR- 35	2.72	146.09	H-Bond (Protein Donor)	false
O3B	OE1	GLU- 55	2.71	174.42	H-Bond (Ligand Donor)	false
O2B	OE2	GLU- 55	2.56	156.18	H-Bond (Ligand Donor)	false
C1B	CB	LYS- 56	4.34	0	Hydrophobic	false
N3A	N	LYS- 56	3.31	130.95	H-Bond (Protein Donor)	false
C7M	CE1	TYR- 73	4.42	0	Hydrophobic	false
C7M	CZ	PHE- 77	3.77	0	Hydrophobic	false
C7M	CB	LYS- 99	3.84	0	Hydrophobic	false
C8M	CB	LYS- 99	4.16	0	Hydrophobic	false
O1A	OG	SER- 107	3.41	156.69	H-Bond (Protein Donor)	false
O1A	N	SER- 107	3.47	146.54	H-Bond (Protein Donor)	false
O2A	N	SER- 107	3.06	150.81	H-Bond (Protein Donor)	false
C3'	CB	SER- 107	3.84	0	Hydrophobic	false
C9	CB	SER- 107	4.02	0	Hydrophobic	false
C7M	CD1	ILE- 110	4.25	0	Hydrophobic	false
C8M	CD1	ILE- 110	4.16	0	Hydrophobic	false
O2'	ND2	ASN- 111	2.92	174.54	H-Bond (Protein Donor)	false
C9A	CB	ASN- 111	3.31	0	Hydrophobic	false
N5	N	GLY- 112	3.07	173.73	H-Bond (Protein Donor)	false
N3	O	SER- 114	2.75	156.69	H-Bond (Ligand Donor)	false
O4	N	SER- 114	2.96	153.14	H-Bond (Protein Donor)	false
N6A	O	VAL- 254	2.87	159.57	H-Bond (Ligand Donor)	false
N1A	N	VAL- 254	2.82	167.48	H-Bond (Protein Donor)	false
C7M	CE3	TRP- 519	3.3	0	Hydrophobic	false
C8M	CB	TRP- 519	3.75	0	Hydrophobic	false
O2P	N	GLY- 553	2.9	156.12	H-Bond (Protein Donor)	false
C1'	CG2	VAL- 564	3.61	0	Hydrophobic	false
O2	N	MET- 565	2.75	155.91	H-Bond (Protein Donor)	false
C2'	CG	MET- 565	4.18	0	Hydrophobic	false
C5'	CD2	PHE- 568	3.74	0	Hydrophobic	false
O2	O	HOH- 644	2.93	143.73	H-Bond (Protein Donor)	false
O1P	O	HOH- 891	2.83	179.97	H-Bond (Protein Donor)	false