Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

1xnz

1.520 Å

X-ray

2004-10-05

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:12.944
Number of residues:29
Including
Standard Amino Acids: 27
Non Standard Amino Acids: 2
Water Molecules: 0
Cofactors:
Metals: MN MN

Cavity properties

LigandabilityVolume (Å3)
0.250293.625

% Hydrophobic% Polar
49.4350.57
According to VolSite

Ligand :
1xnz_1 Structure
HET Code: FCD
Formula: C11H6ClO3
Molecular weight: 221.617 g/mol
DrugBank ID: DB02909
Buried Surface Area:66.95 %
Polar Surface area: 53.27 Å2
Number of
H-Bond Acceptors: 2
H-Bond Donors: 0
Rings: 2
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
-2.89307-1.01228.65747


Binding mode :
What is Poseview ?
  • 2D View
  • 3D View
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
CL2CBCYS- 594.450Hydrophobic
CL2CD2TYR- 624.090Hydrophobic
C4CBHIS- 633.570Hydrophobic
C5CBTYR- 654.460Hydrophobic
CL2CGTYR- 653.620Hydrophobic
CL2SGCYS- 704.190Hydrophobic
OANE2HIS- 1783.23130.25H-Bond
(Protein Donor)
C5CZ3TRP- 2213.350Hydrophobic
OXTMN MN- 2652.030Metal Acceptor
OBMN MN- 2662.210Metal Acceptor
OXTMN MN- 2662.290Metal Acceptor