scPDB - 3m6v entry

Protein Data Bank Entry:

PDB ID : 3m6v

Resolution :1.820 Å

Experimental Method : X-ray

Deposition Date : 2010-03-16

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 F
ID:	RSMF_THET8
AC:	Q5SII2
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	300852
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	15.746
Number of residues:	36
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	6
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.961	803.250

% Hydrophobic	% Polar
42.44	57.56
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	57.29 %
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
13.6453	0.687259	28.5625

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	ALA- 109	2.9	149.36	H-Bond (Ligand Donor)	false
C1'	CB	ALA- 109	4.07	0	Hydrophobic	false
C4'	CB	ALA- 109	3.66	0	Hydrophobic	false
O	N	GLY- 113	3.03	154.94	H-Bond (Protein Donor)	false
O	N	GLY- 114	2.9	159.13	H-Bond (Protein Donor)	false
OXT	N	LYS- 115	3.01	153.94	H-Bond (Protein Donor)	false
OXT	NZ	LYS- 115	3.55	0	Ionic (Protein Cationic)	false
O3'	OE2	GLU- 133	3.35	126.12	H-Bond (Ligand Donor)	false
O3'	OE1	GLU- 133	2.74	146.24	H-Bond (Ligand Donor)	false
O3'	NE	ARG- 138	2.81	137.21	H-Bond (Protein Donor)	false
O3'	NH2	ARG- 138	3.11	126.78	H-Bond (Protein Donor)	false
C2'	CD	ARG- 138	4.34	0	Hydrophobic	false
N	OD2	ASP- 177	2.87	150.4	H-Bond (Ligand Donor)	false
N	OD2	ASP- 177	2.87	0	Ionic (Ligand Cationic)	false
C5'	CB	PRO- 179	4.17	0	Hydrophobic	false
C1'	CG	PRO- 179	4.49	0	Hydrophobic	false
N	O	HOH- 529	2.77	156.06	H-Bond (Ligand Donor)	false
OXT	O	HOH- 533	3.36	123.48	H-Bond (Protein Donor)	false
N3	O	HOH- 547	2.93	158.92	H-Bond (Protein Donor)	false