scPDB - 3d3x entry

Protein Data Bank Entry:

PDB ID : 3d3x

Resolution :2.250 Å

Experimental Method : X-ray

Deposition Date : 2008-05-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Type E botulinum toxin
ID:	Q9K395_CLOBU
AC:	Q9K395
Organism:	Clostridium butyricum
Reign:	Bacteria
TaxID:	1492
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	42.723
Number of residues:	35
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.125	840.375

% Hydrophobic	% Polar
26.10	73.90
According to VolSite

Ligand :

HET Code:	ARG_ILE_MET_GLU_NH2
Formula:	C22H42N7O6S
Molecular weight:	532.677 g/mol
DrugBank ID:	-
Buried Surface Area:	59.99 %
Polar Surface area:	263.45 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	7
Rings:	0
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	3
Rotatable Bonds:	19

Mass center Coordinates

X	Y	Z
49.5281	56.4274	32.4372

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
CZ	OE1	GLU- 158	2.81	0	Ionic (Ligand Cationic)	false
CZ	OE2	GLU- 158	3.36	0	Ionic (Ligand Cationic)	false
NH1	OE2	GLU- 158	2.83	124.43	H-Bond (Ligand Donor)	false
N	O	THR- 159	3.14	172.04	H-Bond (Ligand Donor)	false
CG2	CB	THR- 159	3.99	0	Hydrophobic	false
CB	CB	ASN- 160	4.24	0	Hydrophobic	false
CD	CB	ASN- 160	4.27	0	Hydrophobic	false
CG2	CE2	PHE- 191	4.5	0	Hydrophobic	false
CG1	CE2	PHE- 191	3.45	0	Hydrophobic	false
CB	CG2	THR- 208	3.65	0	Hydrophobic	false
CG1	CG2	THR- 208	3.57	0	Hydrophobic	false
CD1	CB	HIS- 211	3.9	0	Hydrophobic	false
N	OE1	GLU- 212	2.71	0	Ionic (Ligand Cationic)	false
N	OE2	GLU- 212	2.78	0	Ionic (Ligand Cationic)	false
N	OE2	GLU- 212	2.78	171.67	H-Bond (Ligand Donor)	false
CG	CG2	THR- 246	4.14	0	Hydrophobic	false
O	NH1	ARG- 347	3.08	138.54	H-Bond (Protein Donor)	false
O	NH2	ARG- 347	3.06	139.27	H-Bond (Protein Donor)	false
O	OH	TYR- 350	3.08	164.97	H-Bond (Protein Donor)	false
CG	CE2	TYR- 350	3.5	0	Hydrophobic	false
CG	CG2	ILE- 351	3.98	0	Hydrophobic	false
SD	CD2	TYR- 354	4.47	0	Hydrophobic	false
CE	CE1	TYR- 356	3.42	0	Hydrophobic	false
O	ZN	ZN- 822	2.69	0	Metal Acceptor	false