scPDB - 4oma entry

Protein Data Bank Entry:

PDB ID : 4oma

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2014-01-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Methionine gamma-lyase
ID:	Q84AR1_CITFR
AC:	Q84AR1
Organism:	Citrobacter freundii
Reign:	Bacteria
TaxID:	546
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	24.397
Number of residues:	33
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.903	907.875

% Hydrophobic	% Polar
52.79	47.21
According to VolSite

Ligand :

HET Code:	LCS
Formula:	C11H12N3O7P
Molecular weight:	329.203 g/mol
DrugBank ID:	DB03787
Buried Surface Area:	68.5 %
Polar Surface area:	166.04 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	2
Rings:	2
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
7.185	18.8909	12.6252

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
O3P	N	GLY- 88	3.01	153.94	H-Bond (Protein Donor)	false
C5A	CG1	ILE- 89	3.93	0	Hydrophobic	false
O1P	N	ILE- 89	2.87	163.35	H-Bond (Protein Donor)	false
C2A	CB	TYR- 113	4.2	0	Hydrophobic	false
C5A	CE2	TYR- 113	3.61	0	Hydrophobic	false
C2A	CG	GLU- 156	4.48	0	Hydrophobic	false
N1	OD2	ASP- 185	2.57	173.56	H-Bond (Ligand Donor)	false
C2A	CB	THR- 187	3.74	0	Hydrophobic	false
C2A	CE1	PHE- 188	4.06	0	Hydrophobic	false
C5A	CB	SER- 207	4.01	0	Hydrophobic	false
O3P	OG	SER- 207	2.69	163.34	H-Bond (Protein Donor)	false
O3P	OG1	THR- 209	2.79	152.71	H-Bond (Protein Donor)	false
O	NH1	ARG- 374	2.85	151.19	H-Bond (Protein Donor)	false
O	NH2	ARG- 374	3.01	141.75	H-Bond (Protein Donor)	false