scPDB - 5i9e entry

Protein Data Bank Entry:

PDB ID : 5i9e

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2016-02-20

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 4
ID:	ARP4_YEAST
AC:	P80428
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
C	98 %
D	2 %

Ligand binding site composition:

B-Factor:	99.999
Number of residues:	48
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.510	1947.375

% Hydrophobic	% Polar
38.30	61.70
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	68.71 %
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
-4.93294	260.865	96.3003

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
O2G	N	SER- 23	2.78	171.86	H-Bond (Protein Donor)	false
O3G	OG	SER- 23	2.93	149.22	H-Bond (Protein Donor)	false
O3B	N	SER- 23	3.22	120.79	H-Bond (Protein Donor)	false
O1B	N	TYR- 24	2.97	155.59	H-Bond (Protein Donor)	false
O3B	N	TYR- 24	3.4	131.36	H-Bond (Protein Donor)	false
C3'	CD2	TYR- 24	3.59	0	Hydrophobic	false
C2'	CE2	TYR- 24	3.88	0	Hydrophobic	false
O1B	N	THR- 25	2.98	168.32	H-Bond (Protein Donor)	false
O3'	ND1	HIS- 162	3	136.89	H-Bond (Protein Donor)	false
O2'	OE1	GLN- 240	2.74	164.76	H-Bond (Ligand Donor)	false
N7	NE2	GLN- 240	2.92	154.24	H-Bond (Protein Donor)	false
O2'	NZ	LYS- 243	3.16	176.16	H-Bond (Protein Donor)	false
C4'	CB	THR- 414	4.41	0	Hydrophobic	false
O4'	OG1	THR- 414	2.99	160.6	H-Bond (Protein Donor)	false
O1G	MG	MG- 502	2.06	0	Metal Acceptor	false
O2G	MG	MG- 502	2.5	0	Metal Acceptor	false
O2B	MG	MG- 502	2.2	0	Metal Acceptor	false