scPDB - 4kgk entry

Protein Data Bank Entry:

PDB ID : 4kgk

Resolution :2.950 Å

Experimental Method : X-ray

Deposition Date : 2013-04-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uncharacterized protein
ID:	Q3F0V8_BACTI
AC:	Q3F0V8
Organism:	Bacillus thuringiensis serovar israelensis ATCC 35646
Reign:	Bacteria
TaxID:	339854
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	94 %
B	6 %

Ligand binding site composition:

B-Factor:	62.754
Number of residues:	32
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	4
Water Molecules:	0
Cofactors:	GTP
Metals:	MG MG MG

Cavity properties

Ligandability	Volume (Å3)
0.705	671.625

% Hydrophobic	% Polar
35.68	64.32
According to VolSite

Ligand :

HET Code:	GTP
Formula:	C10H12N5O14P3
Molecular weight:	519.149 g/mol
DrugBank ID:	DB04137
Buried Surface Area:	47.28 %
Polar Surface area:	335.56 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
41.6366	123.054	-17.3458

Binding mode :

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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	PHE- 34	3.25	154.61	H-Bond (Protein Donor)	false
C4'	CB	PHE- 34	4.37	0	Hydrophobic	false
O2B	N	HIS- 35	3.23	132.92	H-Bond (Protein Donor)	false
C1'	CG2	THR- 38	4.24	0	Hydrophobic	false
N3	OG1	THR- 38	3.37	130.07	H-Bond (Ligand Donor)	false
C5'	CB	ASP- 75	4.45	0	Hydrophobic	false
O3G	MG	MG- 302	2.5	0	Metal Acceptor	false
O1B	MG	MG- 302	1.98	0	Metal Acceptor	false
O2A	MG	MG- 302	2.65	0	Metal Acceptor	false
O2A	MG	MG- 303	2.59	0	Metal Acceptor	false