scPDB - 5a04 entry

Protein Data Bank Entry:

PDB ID : 5a04

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2015-04-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glucose-fructose oxidoreductase
ID:	Q9A8X3_CAUCR
AC:	Q9A8X3
Organism:	Caulobacter crescentus
Reign:	Bacteria
TaxID:	190650
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	20.384
Number of residues:	44
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.090	759.375

% Hydrophobic	% Polar
37.33	62.67
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	66.38 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
41.5727	-21.5994	55.1701

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
O3X	N	LEU- 14	2.9	163.98	H-Bond (Protein Donor)	false
O2A	N	TYR- 16	2.82	171.8	H-Bond (Protein Donor)	false
O1N	N	TYR- 17	3.08	161.98	H-Bond (Protein Donor)	false
DuAr	DuAr	TYR- 17	3.71	0	Aromatic Face/Face	false
C5N	CB	TYR- 17	3.64	0	Hydrophobic	false
O1X	N	GLY- 40	3.02	152.66	H-Bond (Protein Donor)	false
O2X	OG1	THR- 41	2.74	156.39	H-Bond (Protein Donor)	false
O2X	NZ	LYS- 44	2.72	165	H-Bond (Protein Donor)	false
O2X	NZ	LYS- 44	2.72	0	Ionic (Protein Cationic)	false
C4D	CG2	ILE- 80	3.94	0	Hydrophobic	false
O3D	OD1	ASN- 83	3.04	167.38	H-Bond (Ligand Donor)	false
O3D	NE2	HIS- 86	2.9	123.99	H-Bond (Protein Donor)	false
C4D	CB	GLU- 103	4.39	0	Hydrophobic	false
N7N	OE1	GLU- 103	2.92	172.17	H-Bond (Ligand Donor)	false
O2D	O	LYS- 104	2.86	160.54	H-Bond (Ligand Donor)	false
O2D	NZ	LYS- 104	3.22	174.63	H-Bond (Protein Donor)	false
C3N	CD	LYS- 104	4.46	0	Hydrophobic	false
O7N	NE	ARG- 132	2.75	152.87	H-Bond (Protein Donor)	false
O7N	NH2	ARG- 132	2.93	139.48	H-Bond (Protein Donor)	false
O1A	NE1	TRP- 171	2.94	129.9	H-Bond (Protein Donor)	false
O3	NE1	TRP- 171	3.01	158.02	H-Bond (Protein Donor)	false
C3D	CZ2	TRP- 171	3.61	0	Hydrophobic	false
C2D	CH2	TRP- 171	4.08	0	Hydrophobic	false
C5D	CZ2	TRP- 171	3.83	0	Hydrophobic	false
O2N	CZ	ARG- 172	3.5	0	Ionic (Protein Cationic)	false
O2N	NH1	ARG- 172	3.25	137.2	H-Bond (Protein Donor)	false
O2N	NH2	ARG- 172	2.87	160.49	H-Bond (Protein Donor)	false
O5D	NH2	ARG- 172	3.42	125.47	H-Bond (Protein Donor)	false
O1N	O	HOH- 2003	2.6	168.59	H-Bond (Protein Donor)	false
O2D	O	HOH- 2086	2.77	156.49	H-Bond (Protein Donor)	false