scPDB - 4bgb entry

Protein Data Bank Entry:

PDB ID : 4bgb

Resolution :1.340 Å

Experimental Method : X-ray

Deposition Date : 2013-03-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Predicted molecular chaperone distantly related to HSP70-fold metalloproteases
ID:	Q8TX37_METKA
AC:	Q8TX37
Organism:	Methanopyrus kandleri
Reign:	Archaea
TaxID:	190192
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	9 %
B	91 %

Ligand binding site composition:

B-Factor:	17.004
Number of residues:	42
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.170	843.750

% Hydrophobic	% Polar
38.40	61.60
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	71.29 %
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
5.56293	-25.83	-12.3288

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
O2B	OG1	THR- 48	3.48	142.41	H-Bond (Protein Donor)	false
O3B	N	THR- 48	2.84	154.96	H-Bond (Protein Donor)	false
O3B	OG1	THR- 48	3.33	120.58	H-Bond (Protein Donor)	false
C5'	CG2	THR- 48	4.01	0	Hydrophobic	false
C3'	CG2	THR- 48	4.09	0	Hydrophobic	false
O2B	N	ALA- 168	2.8	164.91	H-Bond (Protein Donor)	false
C4'	CG2	THR- 191	4.35	0	Hydrophobic	false
C2'	CB	THR- 191	4.45	0	Hydrophobic	false
C1'	CG2	THR- 191	4.48	0	Hydrophobic	false
O3'	OD2	ASP- 195	2.66	144.37	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 195	3.39	147.71	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 195	2.61	164.15	H-Bond (Ligand Donor)	false
C3'	CD2	TYR- 206	4.29	0	Hydrophobic	false
C2'	CB	TYR- 206	3.8	0	Hydrophobic	false
N6	OE2	GLU- 208	2.92	157.22	H-Bond (Ligand Donor)	false
N1	N	GLY- 209	2.86	164.17	H-Bond (Protein Donor)	false
O2A	N	GLY- 298	2.97	174.43	H-Bond (Protein Donor)	false
O1B	MG	MG- 1359	2.66	0	Metal Acceptor	false
O2A	MG	MG- 1359	2.74	0	Metal Acceptor	false
O1A	MG	MG- 1360	2.22	0	Metal Acceptor	false
O1B	O	HOH- 2006	3.03	154.82	H-Bond (Protein Donor)	false