scPDB - 1jgt entry

Protein Data Bank Entry:

PDB ID : 1jgt

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2001-06-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Carboxyethyl-arginine beta-lactam-synthase
ID:	BLS_STRCL
AC:	P0DJQ7
Organism:	Streptomyces clavuligerus
Reign:	Bacteria
TaxID:	1901
EC Number:	6.3.3.4

Chains:

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

Ligand binding site composition:

B-Factor:	26.501
Number of residues:	39
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
1.069	894.375

% Hydrophobic	% Polar
41.51	58.49
According to VolSite

Ligand :

HET Code:	APC
Formula:	C11H14N5O12P3
Molecular weight:	501.176 g/mol
DrugBank ID:	DB02596
Buried Surface Area:	64.47 %
Polar Surface area:	310.64 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-45.1008	102.897	31.9359

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
O2'	O	VAL- 247	2.69	166.07	H-Bond (Ligand Donor)	false
C1'	CG2	VAL- 247	3.94	0	Hydrophobic	false
C3A	CB	SER- 249	4.22	0	Hydrophobic	false
O3G	N	ILE- 252	3.49	121.56	H-Bond (Protein Donor)	false
O1B	OG	SER- 254	3.16	156.63	H-Bond (Protein Donor)	false
C2'	CB	SER- 254	3.94	0	Hydrophobic	false
N6	O	MET- 273	2.69	170.7	H-Bond (Ligand Donor)	false
N1	N	MET- 273	2.88	165.32	H-Bond (Protein Donor)	false
C1'	CD2	LEU- 330	3.56	0	Hydrophobic	false
O2'	N	GLY- 347	3.21	175.83	H-Bond (Protein Donor)	false
C5'	CD1	TYR- 348	3.5	0	Hydrophobic	false
C4'	CB	TYR- 348	3.84	0	Hydrophobic	false
O2G	NZ	LYS- 423	3.19	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 423	2.63	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 423	2.63	153.29	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 443	3.76	0	Ionic (Protein Cationic)	false
O2G	NZ	LYS- 443	3.25	0	Ionic (Protein Cationic)	false
O2G	MG	MG- 901	2.02	0	Metal Acceptor	false
O2B	MG	MG- 901	2.14	0	Metal Acceptor	false
O1A	MG	MG- 901	2.18	0	Metal Acceptor	false
O3G	O	HOH- 1101	2.69	180	H-Bond (Protein Donor)	false