scPDB - 4gvz entry

Protein Data Bank Entry:

PDB ID : 4gvz

Resolution :2.960 Å

Experimental Method : X-ray

Deposition Date : 2012-08-31

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Arginine kinase
ID:	KARG_LIMPO
AC:	P51541
Organism:	Limulus polyphemus
Reign:	Eukaryota
TaxID:	6850
EC Number:	2.7.3.3

Chains:

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

Ligand binding site composition:

B-Factor:	16.514
Number of residues:	42
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.030	421.875

% Hydrophobic	% Polar
45.60	54.40
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	77.58 %
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
-2.85437	-7.55363	20.4574

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
N1	OG	SER- 122	2.99	166.93	H-Bond (Protein Donor)	false
O2B	CZ	ARG- 124	3.36	0	Ionic (Protein Cationic)	false
O2B	NH1	ARG- 124	3.07	134.93	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 124	2.79	148.31	H-Bond (Protein Donor)	false
C1'	CD	ARG- 124	4.35	0	Hydrophobic	false
O3B	NH1	ARG- 126	2.93	133.14	H-Bond (Protein Donor)	false
O3B	NE	ARG- 126	2.58	156.64	H-Bond (Protein Donor)	false
O3B	CZ	ARG- 126	3.17	0	Ionic (Protein Cationic)	false
C1'	CB	HIS- 185	3.86	0	Hydrophobic	false
C5'	CH2	TRP- 221	3.4	0	Hydrophobic	false
O1B	CZ	ARG- 229	3.89	0	Ionic (Protein Cationic)	false
O1B	NH1	ARG- 229	2.93	154.32	H-Bond (Protein Donor)	false
O3B	NE	ARG- 280	2.66	164.06	H-Bond (Protein Donor)	false
O3A	NH2	ARG- 280	2.98	144.09	H-Bond (Protein Donor)	false
O3B	CZ	ARG- 280	3.6	0	Ionic (Protein Cationic)	false
N7	OG	SER- 282	2.82	144.33	H-Bond (Protein Donor)	false
N6	OG	SER- 282	2.99	156.48	H-Bond (Ligand Donor)	false
DuAr	DuAr	HIS- 284	3.38	0	Aromatic Face/Face	false
O2A	NH1	ARG- 309	3.17	148.62	H-Bond (Protein Donor)	false
O2'	O	THR- 311	2.94	162.42	H-Bond (Ligand Donor)	false
O2A	N	GLU- 314	3	145.36	H-Bond (Protein Donor)	false
O1B	MG	MG- 402	2.19	0	Metal Acceptor	false
O1A	MG	MG- 402	2.13	0	Metal Acceptor	false