scPDB - 1ryd entry

Protein Data Bank Entry:

PDB ID : 1ryd

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2003-12-22

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:	GFO_ZYMMO
AC:	Q07982
Organism:	Zymomonas mobilis subsp. mobilis
Reign:	Bacteria
TaxID:	264203
EC Number:	1.1.99.28

Chains:

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

Ligand binding site composition:

B-Factor:	42.734
Number of residues:	48
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.081	1235.250

% Hydrophobic	% Polar
38.25	61.75
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	67.23 %
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
25.5661	31.9444	64.7566

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
O2B	N	LEU- 39	3.39	123.83	H-Bond (Protein Donor)	false
O2X	N	LEU- 39	3.11	145.2	H-Bond (Protein Donor)	false
O2N	N	TYR- 42	3.02	157.96	H-Bond (Protein Donor)	false
DuAr	DuAr	TYR- 42	3.71	0	Aromatic Face/Face	false
C5N	CB	TYR- 42	3.63	0	Hydrophobic	false
O2X	OG	SER- 64	2.77	167.13	H-Bond (Protein Donor)	false
O1X	N	GLY- 65	2.77	159.91	H-Bond (Protein Donor)	false
O2X	NZ	LYS- 69	3.22	0	Ionic (Protein Cationic)	false
O3X	NZ	LYS- 69	2.77	0	Ionic (Protein Cationic)	false
O3X	NZ	LYS- 69	2.77	156.55	H-Bond (Protein Donor)	false
O2B	OH	TYR- 87	2.96	120.99	H-Bond (Protein Donor)	false
O1X	OH	TYR- 87	2.61	146.99	H-Bond (Protein Donor)	false
C1B	CZ	TYR- 87	4.32	0	Hydrophobic	false
C5D	CG2	ILE- 105	4.03	0	Hydrophobic	false
C1B	CD2	LEU- 106	3.37	0	Hydrophobic	false
C5B	CG	PRO- 107	4.44	0	Hydrophobic	false
O3D	OD1	ASN- 108	2.72	154.72	H-Bond (Ligand Donor)	false
O3D	NE2	HIS- 111	2.87	120.53	H-Bond (Protein Donor)	false
C4D	CB	GLU- 128	4.38	0	Hydrophobic	false
N7N	OE1	GLU- 128	3.25	161.94	H-Bond (Ligand Donor)	false
O2D	NZ	LYS- 129	2.97	131.54	H-Bond (Protein Donor)	false
O2D	O	LYS- 129	2.62	150.25	H-Bond (Ligand Donor)	false
O7N	NE	ARG- 157	2.77	159.16	H-Bond (Protein Donor)	false
O2A	NE1	TRP- 199	2.77	135.55	H-Bond (Protein Donor)	false
O3	NE1	TRP- 199	3.32	147.59	H-Bond (Protein Donor)	false
C5D	CZ2	TRP- 199	3.95	0	Hydrophobic	false
C3D	CH2	TRP- 199	3.54	0	Hydrophobic	false
O1N	NH2	ARG- 200	2.72	159.6	H-Bond (Protein Donor)	false
O1N	NH1	ARG- 200	3.12	134.99	H-Bond (Protein Donor)	false
O5D	NH2	ARG- 200	3.35	124.37	H-Bond (Protein Donor)	false
O1N	CZ	ARG- 200	3.35	0	Ionic (Protein Cationic)	false
O2D	O	HOH- 766	2.81	179.99	H-Bond (Protein Donor)	false
O2N	O	HOH- 779	2.91	163.89	H-Bond (Protein Donor)	false
O2D	O	HOH- 791	3.35	145.84	H-Bond (Protein Donor)	false