scPDB - 5fa8 entry

Protein Data Bank Entry:

PDB ID : 5fa8

Resolution :1.300 Å

Experimental Method : X-ray

Deposition Date : 2015-12-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Ribosomal protein L11 methyltransferase, putative
ID:	C3MWA1_SULIM
AC:	C3MWA1
Organism:	Sulfolobus islandicus
Reign:	Archaea
TaxID:	427317
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	17.749
Number of residues:	37
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.518	428.625

% Hydrophobic	% Polar
48.03	51.97
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	67.29 %
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
9.77452	18.4607	-3.67641

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	CD1	TYR- 9	4.44	0	Hydrophobic	false
CE	CB	VAL- 10	4.09	0	Hydrophobic	false
O	N	THR- 12	2.78	171.18	H-Bond (Protein Donor)	false
OXT	OG1	THR- 12	2.67	170.01	H-Bond (Protein Donor)	false
OXT	N	THR- 12	3.48	126.61	H-Bond (Protein Donor)	false
N	OD1	ASP- 34	3.46	0	Ionic (Ligand Cationic)	false
N	OD2	ASP- 34	2.8	0	Ionic (Ligand Cationic)	false
N	OD2	ASP- 34	2.8	159.08	H-Bond (Ligand Donor)	false
N	O	GLY- 36	2.76	158.54	H-Bond (Ligand Donor)	false
O3'	OE1	GLU- 59	2.76	166.55	H-Bond (Ligand Donor)	false
O2'	OE2	GLU- 59	2.64	159.13	H-Bond (Ligand Donor)	false
N3	N	ILE- 60	3.4	133.08	H-Bond (Protein Donor)	false
N6	OD1	ASN- 87	2.93	177.94	H-Bond (Ligand Donor)	false
N1	N	PHE- 88	2.94	160.24	H-Bond (Protein Donor)	false
CG	CD2	PHE- 102	4	0	Hydrophobic	false
CE	CD2	PHE- 102	3.73	0	Hydrophobic	false
C5'	CD2	LEU- 103	4.4	0	Hydrophobic	false
CE	CD1	LEU- 104	3.95	0	Hydrophobic	false
O	O	HOH- 460	2.83	179.97	H-Bond (Protein Donor)	false