scPDB - 1gm8 entry

Protein Data Bank Entry:

PDB ID : 1gm8

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2001-09-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Penicillin G acylase
ID:	PAC_ECOLX
AC:	P06875
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	562
EC Number:	3.5.1.11

Chains:

Chain Name:	Percentage of Residues within binding site
A	19 %
B	81 %

Ligand binding site composition:

B-Factor:	13.932
Number of residues:	27
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.979	448.875

% Hydrophobic	% Polar
51.13	48.87
According to VolSite

Ligand :

HET Code:	SOX
Formula:	C16H19N2O5S
Molecular weight:	351.397 g/mol
DrugBank ID:	DB08559
Buried Surface Area:	46.43 %
Polar Surface area:	113.97 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	3
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
14.4579	-2.04229	3.68271

Binding mode :

What is Poseview ?

2D View
3D View

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
O16	OG	SER- 1	2.53	151.33	H-Bond (Protein Donor)	false
C19	CB	SER- 1	3.99	0	Hydrophobic	false
C19	CB	PRO- 22	4.06	0	Hydrophobic	false
C18	CE1	PHE- 24	3.28	0	Hydrophobic	false
C21	CB	SER- 67	4.01	0	Hydrophobic	false
C18	CB	ALA- 69	4.11	0	Hydrophobic	false
C23	CB	ALA- 69	3.88	0	Hydrophobic	false
C2	CZ	PHE- 71	4.45	0	Hydrophobic	false
C10	CE1	PHE- 71	3.87	0	Hydrophobic	false
C21	CE	MET- 142	3.96	0	Hydrophobic	false
C22	SD	MET- 142	3.67	0	Hydrophobic	false
C23	CB	PHE- 146	4.3	0	Hydrophobic	false
C22	CD1	ILE- 177	3.72	0	Hydrophobic	false
C10	CD1	LEU- 253	4.38	0	Hydrophobic	false