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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:

3d27

2.200 Å

X-ray

2008-05-07

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Methionine aminopeptidase
ID:MAP1_ECOLI
AC:P0AE18
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:18.055
Number of residues:30
Including
Standard Amino Acids: 28
Non Standard Amino Acids: 2
Water Molecules: 0
Cofactors:
Metals: MN MN

Cavity properties

LigandabilityVolume (Å3)
0.687330.750

% Hydrophobic% Polar
52.0447.96
According to VolSite

Ligand :
3d27_1 Structure
HET Code: W29
Formula: C12H12O2S
Molecular weight: 220.287 g/mol
DrugBank ID: DB08718
Buried Surface Area:69.04 %
Polar Surface area: 68.7 Å2
Number of
H-Bond Acceptors: 2
H-Bond Donors: 2
Rings: 2
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
-2.9434713.74658.91013


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
O2MN MN- 12.360Metal Acceptor
O1MN MN- 12.420Metal Acceptor
O2MN MN- 22.010Metal Acceptor
C11CBCYS- 594.470Hydrophobic
C11CD2TYR- 623.680Hydrophobic
C11CBTYR- 654.230Hydrophobic
C12CGTYR- 653.550Hydrophobic
C04SGCYS- 704.320Hydrophobic
C12SGCYS- 703.410Hydrophobic
O1NE2HIS- 1782.52135.44H-Bond
(Ligand Donor)