scPDB - 3ssn entry

Protein Data Bank Entry:

PDB ID : 3ssn

Resolution :2.390 Å

Experimental Method : X-ray

Deposition Date : 2011-07-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Mycinamicin VI 2''-O-methyltransferase
ID:	MYCE_MICGR
AC:	Q83WF2
Organism:	Micromonospora griseorubida
Reign:	Bacteria
TaxID:	28040
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	52 %
C	22 %
D	25 %

Ligand binding site composition:

B-Factor:	48.056
Number of residues:	42
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
1.390	1235.250

% Hydrophobic	% Polar
60.11	39.89
According to VolSite

Ligand :

HET Code:	MVI
Formula:	C35H58NO11
Molecular weight:	668.835 g/mol
DrugBank ID:	-
Buried Surface Area:	53.38 %
Polar Surface area:	165.65 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	5
Rings:	3
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-1.76636	116.966	59.5333

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
CAA	CD1	ILE- 139	4.4	0	Hydrophobic	false
CAB	CG2	ILE- 139	4.34	0	Hydrophobic	false
CAD	CD2	LEU- 143	4.13	0	Hydrophobic	false
CAD	CD1	LEU- 144	4.09	0	Hydrophobic	false
CAW	CB	LEU- 144	4.13	0	Hydrophobic	false
CBO	CD2	LEU- 144	3.89	0	Hydrophobic	false
CAC	CD2	PHE- 172	4.05	0	Hydrophobic	false
CAE	CB	PHE- 172	4.41	0	Hydrophobic	false
CBH	CB	PHE- 172	4	0	Hydrophobic	false
CAF	CD1	LEU- 179	3.85	0	Hydrophobic	false
CBM	CD1	LEU- 179	4.48	0	Hydrophobic	false
OAL	NE2	HIS- 180	2.89	159.74	H-Bond (Ligand Donor)	false
CBQ	CZ	TYR- 208	4.49	0	Hydrophobic	false
CAE	CD2	TRP- 213	4.41	0	Hydrophobic	false
CBG	CE2	TRP- 213	4.46	0	Hydrophobic	false
CBR	CZ2	TRP- 213	4.29	0	Hydrophobic	false
CAB	CH2	TRP- 213	3.96	0	Hydrophobic	false
OAM	NE2	HIS- 278	2.85	165.64	H-Bond (Protein Donor)	false
OAK	NE1	TRP- 306	3.27	156.86	H-Bond (Protein Donor)	false
CBJ	CZ2	TRP- 306	3.78	0	Hydrophobic	false
CAF	CD1	ILE- 379	4.46	0	Hydrophobic	false
CAF	CG2	ILE- 383	3.68	0	Hydrophobic	false
CAU	CD1	ILE- 383	3.52	0	Hydrophobic	false
CAF	CD1	LEU- 390	4.38	0	Hydrophobic	false
CAU	CD1	LEU- 390	4.33	0	Hydrophobic	false
CAV	CD1	LEU- 390	3.83	0	Hydrophobic	false
CBJ	CD2	LEU- 390	4.33	0	Hydrophobic	false
CBQ	CD2	LEU- 390	4.42	0	Hydrophobic	false
CAA	CB	ALA- 393	4.14	0	Hydrophobic	false
CAV	CB	SER- 394	4.36	0	Hydrophobic	false
CBP	CB	SER- 394	4.09	0	Hydrophobic	false
OAN	O	HOH- 454	2.61	179.97	H-Bond (Protein Donor)	false
OAL	MG	MG- 501	2.11	0	Metal Acceptor	false
OAM	MG	MG- 501	2.41	0	Metal Acceptor	false