scPDB - 1olt entry

Protein Data Bank Entry:

PDB ID : 1olt

Resolution :2.070 Å

Experimental Method : X-ray

Deposition Date : 2003-08-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Oxygen-independent coproporphyrinogen III oxidase
ID:	HEMN_ECOLI
AC:	P32131
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	16.537
Number of residues:	33
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.535	779.625

% Hydrophobic	% Polar
34.63	65.37
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	52.56 %
Polar Surface area:	189.77 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
28.0425	62.9295	13.7954

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
C2'	CZ	TYR- 56	4.1	0	Hydrophobic	false
DuAr	DuAr	TYR- 56	3.91	0	Aromatic Face/Face	false
O3'	N	GLY- 112	3.18	167.74	H-Bond (Protein Donor)	false
O2'	O	GLY- 112	2.59	156.19	H-Bond (Ligand Donor)	false
O3'	OE2	GLU- 145	2.59	167.87	H-Bond (Ligand Donor)	false
CE	CZ	PHE- 240	4.17	0	Hydrophobic	false
CB	CZ	PHE- 240	4.11	0	Hydrophobic	false
N6	O	ILE- 329	3	169.09	H-Bond (Ligand Donor)	false
N1	N	ILE- 329	2.82	170.39	H-Bond (Protein Donor)	false