scPDB - 4jf1 entry

Protein Data Bank Entry:

PDB ID : 4jf1

Resolution :1.280 Å

Experimental Method : X-ray

Deposition Date : 2013-02-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Acetylornithine/succinyldiaminopimelate aminotransferase
ID:	ARGD_SALTY
AC:	P40732
Organism:	Salmonella typhimurium
Reign:	Bacteria
TaxID:	99287
EC Number:	2.6.1.11

Chains:

Chain Name:	Percentage of Residues within binding site
A	11 %
B	89 %

Ligand binding site composition:

B-Factor:	9.001
Number of residues:	31
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.534	1896.750

% Hydrophobic	% Polar
43.95	56.05
According to VolSite

Ligand :

HET Code:	PLP
Formula:	C8H8NO6P
Molecular weight:	245.126 g/mol
DrugBank ID:	DB00114
Buried Surface Area:	64.27 %
Polar Surface area:	132.42 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	1
Rings:	1
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
62.5436	38.1454	20.308

Binding mode :

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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
O2P	N	GLY- 108	2.99	147.09	H-Bond (Protein Donor)	false
O3P	OG1	THR- 109	2.63	152.22	H-Bond (Protein Donor)	false
O3P	N	THR- 109	2.82	153.84	H-Bond (Protein Donor)	false
C5A	CE2	PHE- 141	3.89	0	Hydrophobic	false
C4	CE2	PHE- 141	3.19	0	Hydrophobic	false
C2A	CG	GLU- 193	3.77	0	Hydrophobic	false
N1	OD1	ASP- 226	3.2	123.63	H-Bond (Ligand Donor)	false
N1	OD2	ASP- 226	2.65	167.04	H-Bond (Ligand Donor)	false
C2A	CB	VAL- 228	4.27	0	Hydrophobic	false
C4	CG1	VAL- 228	3.67	0	Hydrophobic	false
C5	CG1	VAL- 228	3.69	0	Hydrophobic	false
C2A	CB	GLN- 229	4.29	0	Hydrophobic	false
C3	CB	GLN- 229	4.41	0	Hydrophobic	false
O3	NE2	GLN- 229	2.96	153.78	H-Bond (Protein Donor)	false
O3	O	HOH- 668	3.19	162.99	H-Bond (Protein Donor)	false