scPDB - 3ruv entry

Protein Data Bank Entry:

PDB ID : 3ruv

Resolution :2.240 Å

Experimental Method : X-ray

Deposition Date : 2011-05-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Chaperonin
ID:	Q877G8_METMI
AC:	Q877G8
Organism:	Methanococcus maripaludis
Reign:	Archaea
TaxID:	39152
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	36.474
Number of residues:	45
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.915	600.750

% Hydrophobic	% Polar
48.88	51.12
According to VolSite

Ligand :

HET Code:	ANP
Formula:	C10H13N6O12P3
Molecular weight:	502.164 g/mol
DrugBank ID:	-
Buried Surface Area:	76.11 %
Polar Surface area:	322.68 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
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
17.701	54.7685	-19.3682

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
O2A	N	GLY- 40	2.87	143.01	H-Bond (Protein Donor)	false
O5'	N	GLY- 40	3.1	129.79	H-Bond (Protein Donor)	false
O2G	N	GLY- 61	2.7	168.24	H-Bond (Protein Donor)	false
O1B	N	GLY- 92	2.98	132.37	H-Bond (Protein Donor)	false
O1G	N	THR- 93	3.07	139.94	H-Bond (Protein Donor)	false
O1G	OG1	THR- 93	2.56	166.76	H-Bond (Protein Donor)	false
O2B	N	THR- 95	2.89	158.48	H-Bond (Protein Donor)	false
O2B	OG1	THR- 95	2.74	157.72	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 161	3.31	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 161	3.04	0	Ionic (Protein Cationic)	false
O2'	N	GLY- 404	2.93	168.7	H-Bond (Protein Donor)	false
C4'	CD1	LEU- 444	4.27	0	Hydrophobic	false
C1'	CD1	LEU- 444	4.44	0	Hydrophobic	false
O2'	OE2	GLU- 490	2.71	160.46	H-Bond (Ligand Donor)	false
O3G	MG	MG- 544	2.1	0	Metal Acceptor	false
O1B	MG	MG- 544	2.3	0	Metal Acceptor	false
O1A	MG	MG- 544	2.15	0	Metal Acceptor	false
O3'	O	HOH- 579	3.26	179.95	H-Bond (Protein Donor)	false
O3'	O	HOH- 589	2.81	179.99	H-Bond (Protein Donor)	false