scPDB - 3o9z entry

Protein Data Bank Entry:

PDB ID : 3o9z

Resolution :1.450 Å

Experimental Method : X-ray

Deposition Date : 2010-08-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Lipopolysaccaride biosynthesis protein wbpB
ID:	Q72KX8_THET2
AC:	Q72KX8
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	262724
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	6 %
C	6 %
D	88 %

Ligand binding site composition:

B-Factor:	29.951
Number of residues:	53
Including
Standard Amino Acids:	50
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.936	1431.000

% Hydrophobic	% Polar
39.15	60.85
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	72.64 %
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
48.3402	43.1402	49.8562

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
O1A	N	TYR- 12	3.01	167.38	H-Bond (Protein Donor)	false
O2N	N	ILE- 13	3.33	153.09	H-Bond (Protein Donor)	false
C5D	CG2	ILE- 13	3.75	0	Hydrophobic	false
C3N	CD1	ILE- 13	3.58	0	Hydrophobic	false
O3B	OD1	ASP- 33	2.65	123.9	H-Bond (Ligand Donor)	false
O3B	OD2	ASP- 33	3.21	162.9	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 33	2.68	174.71	H-Bond (Ligand Donor)	false
C2B	CG	PRO- 34	3.41	0	Hydrophobic	false
O3B	ND2	ASN- 37	3.03	130.8	H-Bond (Protein Donor)	false
N6A	OE2	GLU- 55	3.23	125.79	H-Bond (Ligand Donor)	false
C1B	CG	PRO- 79	4.4	0	Hydrophobic	false
O3D	OD1	ASN- 80	2.65	158.46	H-Bond (Ligand Donor)	false
N1A	NE2	GLN- 86	2.85	124.92	H-Bond (Protein Donor)	false
C4D	CG	GLU- 100	4.26	0	Hydrophobic	false
C2D	CD	LYS- 101	4.5	0	Hydrophobic	false
C3N	CD	LYS- 101	4.31	0	Hydrophobic	false
O2D	O	LYS- 101	3.09	165.45	H-Bond (Ligand Donor)	false
O2D	NZ	LYS- 101	2.76	171.79	H-Bond (Protein Donor)	false
O7N	NE2	GLN- 129	3.02	176.25	H-Bond (Protein Donor)	false
O2A	NE1	TRP- 168	2.73	150.17	H-Bond (Protein Donor)	false
O3	NE1	TRP- 168	3.4	139.94	H-Bond (Protein Donor)	false
C3D	CH2	TRP- 168	3.89	0	Hydrophobic	false
O1N	NZ	LYS- 169	2.86	167.3	H-Bond (Protein Donor)	false
O1N	NZ	LYS- 169	2.86	0	Ionic (Protein Cationic)	false