scPDB - 1nw5 entry

Protein Data Bank Entry:

PDB ID : 1nw5

Resolution :2.050 Å

Experimental Method : X-ray

Deposition Date : 2003-02-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Modification methylase RsrI
ID:	MTR1_RHOSH
AC:	P14751
Organism:	Rhodobacter sphaeroides
Reign:	Bacteria
TaxID:	1063
EC Number:	2.1.1.72

Chains:

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

Ligand binding site composition:

B-Factor:	24.292
Number of residues:	38
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.670	496.125

% Hydrophobic	% Polar
53.06	46.94
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	67.1 %
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
27.5323	22.6763	-3.47456

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	OD2	ASP- 46	2.76	152.94	H-Bond (Ligand Donor)	false
N1	N	CYS- 47	2.97	149.2	H-Bond (Protein Donor)	false
N	OD2	ASP- 65	2.66	168.71	H-Bond (Ligand Donor)	false
N	OD2	ASP- 65	2.66	0	Ionic (Ligand Cationic)	false
CG	CB	ASP- 65	4.18	0	Hydrophobic	false
O3'	NE2	HIS- 223	2.81	158.21	H-Bond (Protein Donor)	false
CE	CB	THR- 225	3.91	0	Hydrophobic	false
OXT	N	LYS- 227	2.71	156.62	H-Bond (Protein Donor)	false
C1'	CD1	PHE- 250	4.26	0	Hydrophobic	false
C4'	CB	PHE- 250	3.91	0	Hydrophobic	false
O	OG	SER- 253	2.86	141.45	H-Bond (Protein Donor)	false
O	N	SER- 253	2.69	148.96	H-Bond (Protein Donor)	false
OXT	OG	SER- 253	3.5	162.49	H-Bond (Protein Donor)	false
O3'	OD2	ASP- 271	2.57	138.33	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 271	2.74	158.67	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 271	3.44	144.15	H-Bond (Ligand Donor)	false
N3	N	ALA- 272	3.22	145.14	H-Bond (Protein Donor)	false
O3'	O	HOH- 614	3.44	122.78	H-Bond (Protein Donor)	false