scPDB - 1nv8 entry

Protein Data Bank Entry:

PDB ID : 1nv8

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2003-02-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Release factor glutamine methyltransferase
ID:	PRMC_THEMA
AC:	Q9WYV8
Organism:	Thermotoga maritima
Reign:	Bacteria
TaxID:	243274
EC Number:	2.1.1.297

Chains:

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

Ligand binding site composition:

B-Factor:	33.560
Number of residues:	41
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.838	475.875

% Hydrophobic	% Polar
49.65	50.35
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	73.51 %
Polar Surface area:	189.77 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-5.98833	19.8098	-37.7437

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
SD	CG	PHE- 100	3.58	0	Hydrophobic	false
CE	CZ	PHE- 100	3.73	0	Hydrophobic	false
N	O	GLY- 129	3.15	151.41	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 151	2.53	125.55	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 151	3.12	165.29	H-Bond (Ligand Donor)	false
C1'	CG2	VAL- 152	4.39	0	Hydrophobic	false
N1	N	PHE- 180	2.93	153.87	H-Bond (Protein Donor)	false
OXT	ND2	ASN- 197	2.91	161.12	H-Bond (Protein Donor)	false
SD	CB	ALA- 218	3.86	0	Hydrophobic	false
C3'	CB	ALA- 218	3.71	0	Hydrophobic	false
N	O	HOH- 404	3.15	122.92	H-Bond (Ligand Donor)	false
N	O	HOH- 406	2.74	169.07	H-Bond (Ligand Donor)	false
O	O	HOH- 409	3.05	179.95	H-Bond (Protein Donor)	false