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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

1olt

2.070 Å

X-ray

2003-08-13

Interactomes:
Molecular Function:
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
A100 %


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

LigandabilityVolume (Å3)
0.535779.625

% Hydrophobic% Polar
34.6365.37
According to VolSite

Ligand :
1olt_2 Structure
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

XYZ
28.042562.929513.7954


Binding mode :
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Binding mode
BioSolveIT 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
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
C2'CZTYR- 564.10Hydrophobic
DuArDuArTYR- 563.910Aromatic Face/Face
O3'NGLY- 1123.18167.74H-Bond
(Protein Donor)
O2'OGLY- 1122.59156.19H-Bond
(Ligand Donor)
O3'OE2GLU- 1452.59167.87H-Bond
(Ligand Donor)
CECZPHE- 2404.170Hydrophobic
CBCZPHE- 2404.110Hydrophobic
N6OILE- 3293169.09H-Bond
(Ligand Donor)
N1NILE- 3292.82170.39H-Bond
(Protein Donor)