scPDB - 3gwz entry

Protein Data Bank Entry:

PDB ID : 3gwz

Resolution :1.910 Å

Experimental Method : X-ray

Deposition Date : 2009-04-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Mitomycin biosynthesis 6-O-methyltransferase
ID:	MMCR_STRLA
AC:	Q9X5T6
Organism:	Streptomyces lavendulae
Reign:	Bacteria
TaxID:	1914
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	22.818
Number of residues:	39
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.872	583.875

% Hydrophobic	% Polar
61.85	38.15
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	75.04 %
Polar Surface area:	212.38 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
36.7943	59.6139	43.6811

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
C5'	CH2	TRP- 146	4.2	0	Hydrophobic	false
C2'	CZ3	TRP- 146	3.95	0	Hydrophobic	false
SD	CZ	PHE- 159	3.86	0	Hydrophobic	false
C3'	CE2	PHE- 159	3.95	0	Hydrophobic	false
SD	CG	MET- 163	3.67	0	Hydrophobic	false
CG	CG	MET- 163	3.76	0	Hydrophobic	false
N	O	GLY- 190	2.69	163.72	H-Bond (Ligand Donor)	false
O3'	OE2	GLU- 213	2.57	169.88	H-Bond (Ligand Donor)	false
O2'	OE2	GLU- 213	3.3	127.27	H-Bond (Ligand Donor)	false
O2'	OE1	GLU- 213	2.56	156.39	H-Bond (Ligand Donor)	false
O2'	NE	ARG- 214	3.09	148.17	H-Bond (Protein Donor)	false
N6	OD1	ASP- 240	2.79	168.52	H-Bond (Ligand Donor)	false
N1	N	PHE- 241	3.04	162.76	H-Bond (Protein Donor)	false
N	O	LYS- 255	2.81	159.98	H-Bond (Ligand Donor)	false
O	NZ	LYS- 255	2.72	171.77	H-Bond (Protein Donor)	false
O	NZ	LYS- 255	2.72	0	Ionic (Protein Cationic)	false
OXT	NZ	LYS- 255	3.58	0	Ionic (Protein Cationic)	false
CG	CB	HIS- 256	4.12	0	Hydrophobic	false
CG	CG2	VAL- 257	4.37	0	Hydrophobic	false
C5'	CG2	VAL- 257	4.15	0	Hydrophobic	false
O4'	O	HOH- 353	3.37	179.98	H-Bond (Protein Donor)	false