scPDB - 1mbz entry

Protein Data Bank Entry:

PDB ID : 1mbz

Resolution :2.470 Å

Experimental Method : X-ray

Deposition Date : 2002-08-04

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
A	100 %

Ligand binding site composition:

B-Factor:	12.028
Number of residues:	53
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	2
Water Molecules:	3
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.751	641.250

% Hydrophobic	% Polar
47.37	52.63
According to VolSite

Ligand :

HET Code:	IOT
Formula:	C18H28N9O10P
Molecular weight:	561.443 g/mol
DrugBank ID:	-
Buried Surface Area:	78.27 %
Polar Surface area:	325.16 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	7
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	2
Rule of Five Violation:	3
Rotatable Bonds:	15

Mass center Coordinates

X	Y	Z
-4.12974	92.1164	64.899

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
O2'	O	VAL- 247	2.56	151.26	H-Bond (Ligand Donor)	false
C2'	CB	SER- 254	3.58	0	Hydrophobic	false
N6	O	MET- 273	2.86	159.32	H-Bond (Ligand Donor)	false
N1	N	MET- 273	2.71	164.43	H-Bond (Protein Donor)	false
CD	CD1	ILE- 323	4.45	0	Hydrophobic	false
CG	CE2	TYR- 326	3.52	0	Hydrophobic	false
C1'	CD2	LEU- 330	3.79	0	Hydrophobic	false
O2'	N	GLY- 347	3.4	152.27	H-Bond (Protein Donor)	false
NX	OH	TYR- 348	3.44	162.27	H-Bond (Ligand Donor)	false
CB	CZ	TYR- 348	3.77	0	Hydrophobic	false
C5'	CD1	TYR- 348	3.82	0	Hydrophobic	false
O	N	GLY- 349	2.7	166.37	H-Bond (Protein Donor)	false
OX3	N	ASP- 351	3.28	126.99	H-Bond (Protein Donor)	false
CD	CG1	ILE- 352	4.14	0	Hydrophobic	false
CG	CG	MET- 357	4.39	0	Hydrophobic	false
NH2	OD1	ASP- 373	3.48	134.24	H-Bond (Ligand Donor)	false
CZ	OE1	GLU- 382	3.84	0	Ionic (Ligand Cationic)	false
NH1	OE1	GLU- 382	2.8	156.94	H-Bond (Ligand Donor)	false
O1A	NZ	LYS- 443	2.86	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 443	3.59	0	Ionic (Protein Cationic)	false
OX1	NZ	LYS- 443	3.45	149.05	H-Bond (Protein Donor)	false
O1A	MG	MG- 603	1.86	0	Metal Acceptor	false
O2A	MG	MG- 604	2.14	0	Metal Acceptor	false
N6	O	HOH- 627	3.37	155.12	H-Bond (Ligand Donor)	false