scPDB - 3wv8 entry

Protein Data Bank Entry:

PDB ID : 3wv8

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2014-05-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Hmd co-occurring protein HcgE
ID:	D9PY12_METTM
AC:	D9PY12
Organism:	Methanothermobacter marburgensis
Reign:	Archaea
TaxID:	79929
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	23.794
Number of residues:	35
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.243	324.000

% Hydrophobic	% Polar
43.75	56.25
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	63.45 %
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
18.3059	-38.7465	22.7678

Binding mode :

What is Poseview ?

2D View
3D View

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
O1A	CZ	ARG- 23	3.93	0	Ionic (Protein Cationic)	false
O1A	N	ARG- 23	2.86	175.89	H-Bond (Protein Donor)	false
O1A	NH1	ARG- 23	2.88	141.77	H-Bond (Protein Donor)	false
O1B	N	LEU- 24	2.87	166.84	H-Bond (Protein Donor)	false
O3'	OD1	ASP- 47	3.14	163.06	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 47	2.56	130.72	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 47	2.56	156.44	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 47	3.42	144.55	H-Bond (Ligand Donor)	false
C2'	CG	GLN- 49	3.63	0	Hydrophobic	false
O3'	NZ	LYS- 69	2.91	172.92	H-Bond (Protein Donor)	false
C2'	CE1	TYR- 91	4.26	0	Hydrophobic	false
N6	O	ILE- 92	2.93	160.63	H-Bond (Ligand Donor)	false
N1	N	ILE- 92	3.05	139.29	H-Bond (Protein Donor)	false
C1'	CG2	ILE- 109	4.37	0	Hydrophobic	false
C5'	CB	ALA- 110	4.02	0	Hydrophobic	false
O4'	N	ALA- 110	3.31	153.13	H-Bond (Protein Donor)	false
O1A	O	HOH- 404	2.57	153.99	H-Bond (Protein Donor)	false
O1B	O	HOH- 415	2.66	149.63	H-Bond (Protein Donor)	false