scPDB - 1d0m entry

Protein Data Bank Entry:

PDB ID : 1d0m

Resolution :2.470 Å

Experimental Method : X-ray

Deposition Date : 1999-09-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Membrane-bound lytic murein transglycosylase B
ID:	MLTB_ECOLI
AC:	P41052
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	4.2.2.n1

Chains:

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

Ligand binding site composition:

B-Factor:	23.637
Number of residues:	32
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.659	648.000

% Hydrophobic	% Polar
27.60	72.40
According to VolSite

Ligand :

HET Code:	BLG
Formula:	C16H28N3O14S2
Molecular weight:	550.535 g/mol
DrugBank ID:	DB02595
Buried Surface Area:	50.78 %
Polar Surface area:	294.34 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	6
Rings:	2
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
6.23031	23.4034	12.1008

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
O9	OE2	GLU- 162	2.72	168.53	H-Bond (Ligand Donor)	false
O6	NH2	ARG- 188	3.21	142.12	H-Bond (Protein Donor)	false
O6	OH	TYR- 191	3.15	129.04	H-Bond (Ligand Donor)	false
O10	OG	SER- 216	2.56	165.33	H-Bond (Protein Donor)	false
OS2	N	PHE- 217	3.46	158.06	H-Bond (Protein Donor)	false
C9	CB	GLN- 225	4.11	0	Hydrophobic	false
C8	CD1	PHE- 226	3.88	0	Hydrophobic	false
C1	CG	MET- 227	4.13	0	Hydrophobic	false
CG	SD	MET- 227	4.39	0	Hydrophobic	false
O7	N	MET- 227	3.09	170.63	H-Bond (Protein Donor)	false
O7	OG	SER- 230	2.66	149.39	H-Bond (Protein Donor)	false
C8	CE2	TYR- 259	3.71	0	Hydrophobic	false
O3	OH	TYR- 259	2.84	173.45	H-Bond (Ligand Donor)	false
N2	O	TYR- 338	2.83	148.04	H-Bond (Ligand Donor)	false
C8	CZ	TYR- 338	3.41	0	Hydrophobic	false
C9	CE1	TYR- 338	4	0	Hydrophobic	false
O9	ND2	ASN- 339	3.05	149.64	H-Bond (Protein Donor)	false