scPDB - 1mb9 entry

Protein Data Bank Entry:

PDB ID : 1mb9

Resolution :2.110 Å

Experimental Method : X-ray

Deposition Date : 2002-08-02

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:	18.776
Number of residues:	41
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
1.011	779.625

% Hydrophobic	% Polar
50.22	49.78
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	64.17 %
Polar Surface area:	319.88 Å2

Number of
H-Bond Acceptors:	17
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
-44.8256	102.642	31.4539

Binding mode :

What is Poseview ?

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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	2.95	149.53	H-Bond (Ligand Donor)	false
C1'	CG2	VAL- 247	3.71	0	Hydrophobic	false
O3B	N	ASP- 253	3.44	148.97	H-Bond (Protein Donor)	false
O1B	OG	SER- 254	2.82	147.78	H-Bond (Protein Donor)	false
O1B	N	SER- 254	2.7	159.16	H-Bond (Protein Donor)	false
C2'	CB	SER- 254	4	0	Hydrophobic	false
N6	O	MET- 273	2.75	162.64	H-Bond (Ligand Donor)	false
N1	N	MET- 273	2.85	162.83	H-Bond (Protein Donor)	false
C1'	CD1	LEU- 330	3.73	0	Hydrophobic	false
O2'	N	GLY- 347	2.64	174.42	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 423	3.25	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 423	3.16	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 423	3.16	172.16	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 443	3.54	0	Ionic (Protein Cationic)	false
O2G	NZ	LYS- 443	2.66	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 443	3.35	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 443	3.78	0	Ionic (Protein Cationic)	false
O2G	NZ	LYS- 443	2.66	153.55	H-Bond (Protein Donor)	false
O2G	MG	MG- 601	2.05	0	Metal Acceptor	false
O2A	MG	MG- 601	2.32	0	Metal Acceptor	false
O3A	MG	MG- 601	2.06	0	Metal Acceptor	false
O1G	MG	MG- 602	2.07	0	Metal Acceptor	false
O2B	MG	MG- 602	2.01	0	Metal Acceptor	false
O1A	MG	MG- 602	2.51	0	Metal Acceptor	false
O3G	O	HOH- 904	2.51	179.98	H-Bond (Protein Donor)	false