scPDB - 2p9k entry

Protein Data Bank Entry:

PDB ID : 2p9k

Resolution :2.590 Å

Experimental Method : X-ray

Deposition Date : 2007-03-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Actin-related protein 2
ID:	ARP2_BOVIN
AC:	A7MB62
Organism:	Bos taurus
Reign:	Eukaryota
TaxID:	9913
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	43.649
Number of residues:	42
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	CA

Cavity properties

Ligandability	Volume (Å3)
0.095	583.875

% Hydrophobic	% Polar
39.31	60.69
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	66.67 %
Polar Surface area:	319.88 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-21.039	27.2816	29.5241

Binding mode :

What is Poseview ?

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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
O1G	OG1	THR- 15	3.34	143.01	H-Bond (Protein Donor)	false
O3G	OG1	THR- 15	3.44	120.83	H-Bond (Protein Donor)	false
O3G	N	THR- 15	3.09	157.83	H-Bond (Protein Donor)	false
O3B	N	THR- 15	3.12	131.82	H-Bond (Protein Donor)	false
O2B	N	GLY- 16	3.1	144.86	H-Bond (Protein Donor)	false
O2B	N	PHE- 17	2.82	171.3	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 19	2.74	126.27	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 19	2.94	167.18	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 19	2.74	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 19	3.4	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 19	2.94	0	Ionic (Protein Cationic)	false
O1G	N	ASP- 161	3.45	142.78	H-Bond (Protein Donor)	false
O3B	N	ASP- 161	3.37	149.75	H-Bond (Protein Donor)	false
O3'	OD1	ASP- 161	3.06	154.8	H-Bond (Ligand Donor)	false
C4'	CB	ASP- 161	4	0	Hydrophobic	false
O1G	N	GLY- 162	3.17	163.94	H-Bond (Protein Donor)	false
C2'	CD	ARG- 214	4.39	0	Hydrophobic	false
O3'	NZ	LYS- 217	3.22	120.78	H-Bond (Protein Donor)	false
O2'	NZ	LYS- 217	2.86	167.92	H-Bond (Protein Donor)	false
O2'	OE2	GLU- 218	2.77	164.36	H-Bond (Ligand Donor)	false
O1A	N	GLY- 306	3.15	167.01	H-Bond (Protein Donor)	false
O5'	N	GLY- 306	3.44	128.76	H-Bond (Protein Donor)	false
O1B	CA	CA- 501	2.65	0	Metal Acceptor	false
N3	O	HOH- 607	2.76	160.78	H-Bond (Protein Donor)	false