scPDB - 3a9w entry

Protein Data Bank Entry:

PDB ID : 3a9w

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 2009-11-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NDP-sugar epimerase
ID:	Q97BK3_THEVO
AC:	Q97BK3
Organism:	Thermoplasma volcanium
Reign:	Archaea
TaxID:	273116
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	21.425
Number of residues:	55
Including
Standard Amino Acids:	51
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.408	884.250

% Hydrophobic	% Polar
58.02	41.98
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	71.8 %
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
-27.0306	29.9905	16.7609

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
N7N	OE1	GLN- 10	2.67	161.92	H-Bond (Ligand Donor)	false
O1N	N	ILE- 11	2.84	169.43	H-Bond (Protein Donor)	false
O3B	OD2	ASP- 32	2.58	153.9	H-Bond (Ligand Donor)	false
O3B	OD1	ASP- 32	3.31	145.01	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 32	3.03	151.11	H-Bond (Ligand Donor)	false
N6A	OD2	ASP- 47	2.71	150.89	H-Bond (Ligand Donor)	false
N1A	N	VAL- 48	3	148.84	H-Bond (Protein Donor)	false
O3D	O	LEU- 69	3.3	122.75	H-Bond (Ligand Donor)	false
C5D	CB	LEU- 69	4.18	0	Hydrophobic	false
C3D	CD2	LEU- 73	3.9	0	Hydrophobic	false
C2D	CG	LEU- 73	4.39	0	Hydrophobic	false
C4D	CG	PRO- 110	3.54	0	Hydrophobic	false
C5N	CB	THR- 112	3.64	0	Hydrophobic	false
C2D	CE1	PHE- 137	4.38	0	Hydrophobic	false
O3D	NZ	LYS- 141	2.75	136.92	H-Bond (Protein Donor)	false
C5N	CB	TYR- 164	3.44	0	Hydrophobic	false
O7N	N	ILE- 167	3.17	142.96	H-Bond (Protein Donor)	false
C3N	CD1	ILE- 167	4.21	0	Hydrophobic	false
O7N	N	THR- 318	3.04	159.43	H-Bond (Protein Donor)	false
C4N	CG2	THR- 318	3.2	0	Hydrophobic	false