scPDB - 3vpb entry

Protein Data Bank Entry:

PDB ID : 3vpb

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2012-02-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glutamate--LysW ligase ArgX
ID:	ARGX_SULTO
AC:	Q970U6
Organism:	Sulfolobus tokodaii
Reign:	Archaea
TaxID:	273063
EC Number:	6.3.2

Chains:

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

Ligand binding site composition:

B-Factor:	21.305
Number of residues:	37
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.026	347.625

% Hydrophobic	% Polar
40.78	59.22
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	80.18 %
Polar Surface area:	260.7 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
15.3935	-7.97459	-9.1033

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
O1B	NZ	LYS- 87	2.85	173.64	H-Bond (Protein Donor)	false
O3A	NZ	LYS- 87	3.38	124.82	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 87	2.85	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 87	3.95	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 127	2.8	169.63	H-Bond (Protein Donor)	false
N7	NZ	LYS- 127	3.07	153.23	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 127	2.8	0	Ionic (Protein Cationic)	false
O3B	N	GLY- 134	2.77	134.46	H-Bond (Protein Donor)	false
C5'	CG2	VAL- 137	4.14	0	Hydrophobic	false
N6	OE1	GLN- 167	2.93	166.08	H-Bond (Ligand Donor)	false
N6	O	GLU- 168	2.86	152.59	H-Bond (Ligand Donor)	false
N1	N	ILE- 170	2.91	171.05	H-Bond (Protein Donor)	false
O3'	OD2	ASP- 176	2.56	147.84	H-Bond (Ligand Donor)	false
C4'	CB	ARG- 200	3.86	0	Hydrophobic	false
C1'	CG	ARG- 200	4.32	0	Hydrophobic	false
O2'	N	ALA- 201	3.09	133.46	H-Bond (Protein Donor)	false
O2B	ND2	ASN- 202	2.98	158.34	H-Bond (Protein Donor)	false
C2'	CD2	LEU- 239	4.26	0	Hydrophobic	false
O1A	ND2	ASN- 249	3	127.06	H-Bond (Protein Donor)	false
O2B	MG	MG- 502	2.17	0	Metal Acceptor	false
O2A	MG	MG- 502	2.16	0	Metal Acceptor	false
O3'	O	HOH- 710	3.42	120.49	H-Bond (Ligand Donor)	false