scPDB - 5k0s entry

Protein Data Bank Entry:

PDB ID : 5k0s

Resolution :2.450 Å

Experimental Method : X-ray

Deposition Date : 2016-05-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Methionine--tRNA ligase
ID:	SYM_BRUSU
AC:	P59078
Organism:	Brucella suis biovar 1
Reign:	Bacteria
TaxID:	204722
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	36.987
Number of residues:	35
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.023	695.250

% Hydrophobic	% Polar
50.49	49.51
According to VolSite

Ligand :

HET Code:	0OU
Formula:	C19H20Cl2N3O
Molecular weight:	377.288 g/mol
DrugBank ID:	-
Buried Surface Area:	64.58 %
Polar Surface area:	57.74 Å2

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

Mass center Coordinates

X	Y	Z
28.3234	6.07596	11.4704

Binding mode :

What is Poseview ?

2D View
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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
CL2	CB	ALA- 11	3.92	0	Hydrophobic	false
CL2	CG1	ILE- 12	3.58	0	Hydrophobic	false
CAL	CG	TYR- 14	3.63	0	Hydrophobic	false
CAN	CD1	TYR- 14	3.73	0	Hydrophobic	false
NAQ	OD2	ASP- 51	2.76	126.75	H-Bond (Ligand Donor)	false
NAR	OD1	ASP- 51	3.02	161.34	H-Bond (Ligand Donor)	false
NAR	OD2	ASP- 51	3.21	134.04	H-Bond (Ligand Donor)	false
CAF	CB	HIS- 53	3.47	0	Hydrophobic	false
CL1	CG2	VAL- 229	4.13	0	Hydrophobic	false
CAI	CG2	VAL- 229	4.38	0	Hydrophobic	false
CAF	CB	VAL- 229	3.92	0	Hydrophobic	false
CAY	CB	VAL- 229	3.54	0	Hydrophobic	false
CL1	CE3	TRP- 230	3.72	0	Hydrophobic	false
CAD	CB	ASP- 232	3.84	0	Hydrophobic	false
CAS	CB	ALA- 233	3.81	0	Hydrophobic	false
CAH	CB	ALA- 233	3.5	0	Hydrophobic	false
CL1	CG	LEU- 234	4.15	0	Hydrophobic	false
CAH	CD2	LEU- 234	3.8	0	Hydrophobic	false
CL2	CZ	TYR- 237	4.27	0	Hydrophobic	false
CAU	CG2	ILE- 265	4.17	0	Hydrophobic	false
CAJ	CD1	ILE- 265	3.97	0	Hydrophobic	false
CL1	CD2	PHE- 268	3.94	0	Hydrophobic	false