scPDB - 1sqf entry

Protein Data Bank Entry:

PDB ID : 1sqf

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2004-03-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Ribosomal RNA small subunit methyltransferase B
ID:	RSMB_ECOLI
AC:	P36929
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	2.1.1.176

Chains:

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

Ligand binding site composition:

B-Factor:	19.921
Number of residues:	31
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.532	648.000

% Hydrophobic	% Polar
34.90	65.10
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	65.15 %
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
6.93119	2.42956	22.9201

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
N	O	CYS- 254	2.85	165.85	H-Bond (Ligand Donor)	false
C1'	CB	CYS- 254	4.14	0	Hydrophobic	false
C4'	CB	CYS- 254	3.77	0	Hydrophobic	false
O	N	GLY- 258	3.07	132.85	H-Bond (Protein Donor)	false
O	N	GLY- 259	3.02	155.46	H-Bond (Protein Donor)	false
OXT	NZ	LYS- 260	2.99	0	Ionic (Protein Cationic)	false
OXT	N	LYS- 260	3.22	147.87	H-Bond (Protein Donor)	false
O3'	OD2	ASP- 277	2.7	156.68	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 277	2.91	166.94	H-Bond (Ligand Donor)	false
C1'	CG2	ILE- 278	4.46	0	Hydrophobic	false
N3	N	ILE- 278	3.38	146.75	H-Bond (Protein Donor)	false
C3'	CD	ARG- 282	4.22	0	Hydrophobic	false
N6	OD1	ASP- 303	2.9	155.25	H-Bond (Ligand Donor)	false
N1	N	GLY- 304	2.89	165.09	H-Bond (Protein Donor)	false
N	OD2	ASP- 322	2.6	163.02	H-Bond (Ligand Donor)	false
N	OD2	ASP- 322	2.6	0	Ionic (Ligand Cationic)	false
OXT	O	HOH- 443	2.93	164.75	H-Bond (Protein Donor)	false
N	O	HOH- 468	3.1	144.52	H-Bond (Ligand Donor)	false