scPDB - 1jq5 entry

Protein Data Bank Entry:

PDB ID : 1jq5

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2001-08-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glycerol dehydrogenase
ID:	GLDA_GEOSE
AC:	P32816
Organism:	Geobacillus stearothermophilus
Reign:	Bacteria
TaxID:	1422
EC Number:	1.1.1.6

Chains:

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

Ligand binding site composition:

B-Factor:	28.928
Number of residues:	51
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
1.380	1150.875

% Hydrophobic	% Polar
54.84	45.16
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	63.38 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
25.8049	29.6243	22.5745

Binding mode :

What is Poseview ?

2D View
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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
O2B	OD2	ASP- 39	2.71	156.9	H-Bond (Ligand Donor)	false
C2B	CG2	VAL- 42	4.25	0	Hydrophobic	false
O2N	N	GLY- 96	2.9	164.92	H-Bond (Protein Donor)	false
O1A	N	LYS- 97	2.93	158.8	H-Bond (Protein Donor)	false
O3D	NZ	LYS- 97	2.97	151.79	H-Bond (Protein Donor)	false
C4D	CG	LYS- 97	3.91	0	Hydrophobic	false
N7N	OD2	ASP- 100	3.21	173.15	H-Bond (Ligand Donor)	false
N7N	OD1	ASP- 100	2.94	121.94	H-Bond (Ligand Donor)	false
N7A	OG1	THR- 118	2.56	166.59	H-Bond (Protein Donor)	false
N6A	O	THR- 118	2.92	134	H-Bond (Ligand Donor)	false
O2N	OG	SER- 121	2.61	140.36	H-Bond (Protein Donor)	false
C5D	CG2	THR- 122	4.07	0	Hydrophobic	false
C5N	CB	THR- 122	3.77	0	Hydrophobic	false
C3N	CB	ALA- 124	3.36	0	Hydrophobic	false
O7N	OG	SER- 127	2.76	156.05	H-Bond (Protein Donor)	false
N7N	O	LEU- 129	2.73	143.49	H-Bond (Ligand Donor)	false
C2D	CG2	VAL- 131	4.41	0	Hydrophobic	false
C3N	CG2	VAL- 131	4.18	0	Hydrophobic	false
C3D	CE1	TYR- 133	4.31	0	Hydrophobic	false
O2D	OH	TYR- 133	2.86	164.22	H-Bond (Ligand Donor)	false
C1B	CD1	LEU- 166	4.29	0	Hydrophobic	false
C5D	CB	HIS- 274	4.24	0	Hydrophobic	false
O3D	O	HOH- 411	2.74	162.63	H-Bond (Ligand Donor)	false
O1N	O	HOH- 413	2.99	179.97	H-Bond (Protein Donor)	false