scPDB - 3t7v entry

Protein Data Bank Entry:

PDB ID : 3t7v

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2011-07-31

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	3-methylornithine synthase
ID:	PYLB_METBF
AC:	Q46E78
Organism:	Methanosarcina barkeri
Reign:	Archaea
TaxID:	269797
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	15.236
Number of residues:	45
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	2
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.526	459.000

% Hydrophobic	% Polar
47.06	52.94
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	72.25 %
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
46.8413	34.9197	1.67893

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
N6	O	PHE- 77	3.07	127.87	H-Bond (Ligand Donor)	false
C3'	CE1	PHE- 77	3.92	0	Hydrophobic	false
CE	CG2	THR- 114	3.82	0	Hydrophobic	false
CG	CG2	THR- 114	4.14	0	Hydrophobic	false
N	O	MET- 115	3.13	141.6	H-Bond (Ligand Donor)	false
CB	CB	SER- 146	4.42	0	Hydrophobic	false
C4'	CD2	TYR- 169	4.16	0	Hydrophobic	false
O3'	OE2	GLU- 171	2.51	143.17	H-Bond (Ligand Donor)	false
O2'	OE1	GLU- 171	2.67	160.2	H-Bond (Ligand Donor)	false
O	CZ	ARG- 182	3.44	0	Ionic (Protein Cationic)	false
O	NH1	ARG- 182	3.27	126.87	H-Bond (Protein Donor)	false
O	NH2	ARG- 182	2.72	146.4	H-Bond (Protein Donor)	false
O3'	NH2	ARG- 182	3.1	138.68	H-Bond (Protein Donor)	false
OXT	NH2	ARG- 190	2.93	163.96	H-Bond (Protein Donor)	false
OXT	CZ	ARG- 190	3.95	0	Ionic (Protein Cationic)	false
C1'	SD	MET- 237	4	0	Hydrophobic	false
N6	O	LEU- 240	2.86	164.92	H-Bond (Ligand Donor)	false
N1	N	LEU- 240	3.09	177.02	H-Bond (Protein Donor)	false
CE	CG2	VAL- 310	3.81	0	Hydrophobic	false
C5'	CG1	VAL- 310	4.14	0	Hydrophobic	false
C1'	CG1	VAL- 310	4.32	0	Hydrophobic	false
OXT	O	HOH- 354	2.86	153.5	H-Bond (Protein Donor)	false
CE	CG2	MD0- 993	3.56	0	Hydrophobic	false