scPDB - 4ei7 entry

Protein Data Bank Entry:

PDB ID : 4ei7

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2012-04-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Plasmid replication protein RepX
ID:	REPX_BACC1
AC:	Q74P24
Organism:	Bacillus cereus
Reign:	Bacteria
TaxID:	222523
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	97 %
B	3 %

Ligand binding site composition:

B-Factor:	23.348
Number of residues:	44
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.034	1424.250

% Hydrophobic	% Polar
32.46	67.54
According to VolSite

Ligand :

HET Code:	GDP
Formula:	C10H12N5O11P2
Molecular weight:	440.177 g/mol
DrugBank ID:	DB04315
Buried Surface Area:	61.86 %
Polar Surface area:	276.39 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
18.1133	35.4038	50.3748

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
O1B	N	MET- 25	2.8	175.31	H-Bond (Protein Donor)	false
O1A	N	GLY- 26	2.65	155.96	H-Bond (Protein Donor)	false
O3B	N	GLY- 124	2.81	137.82	H-Bond (Protein Donor)	false
O3B	N	THR- 125	3.02	140.52	H-Bond (Protein Donor)	false
O2B	N	GLY- 126	2.71	155.39	H-Bond (Protein Donor)	false
O2'	OE2	GLU- 155	2.67	156.7	H-Bond (Ligand Donor)	false
O2'	OE1	GLU- 155	3.22	122.27	H-Bond (Ligand Donor)	false
O2'	ND2	ASN- 185	3.23	127.1	H-Bond (Protein Donor)	false
N3	ND2	ASN- 185	3.46	147.63	H-Bond (Protein Donor)	false
N2	OD1	ASN- 185	3.25	141.32	H-Bond (Ligand Donor)	false
N2	OG	SER- 208	3.38	127.53	H-Bond (Ligand Donor)	false
O6	ND2	ASN- 209	3.07	160.57	H-Bond (Protein Donor)	false
N1	OD1	ASN- 209	2.68	156.61	H-Bond (Ligand Donor)	false
O1A	O	HOH- 610	2.77	138.98	H-Bond (Protein Donor)	false
O2B	O	HOH- 627	2.57	134.71	H-Bond (Protein Donor)	false
O3B	O	HOH- 662	2.67	179.98	H-Bond (Protein Donor)	false