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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:

1xuz

2.200 Å

X-ray

2004-10-26

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Capsule biosynthesis protein
ID:Q57265_NEIME
AC:Q57265
Organism:Neisseria meningitidis
Reign:Bacteria
TaxID:487
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:12.612
Number of residues:30
Including
Standard Amino Acids: 26
Non Standard Amino Acids: 2
Water Molecules: 2
Cofactors:
Metals: MN

Cavity properties

LigandabilityVolume (Å3)
0.753621.000

% Hydrophobic% Polar
50.5449.46
According to VolSite

Ligand :
1xuz_1 Structure
HET Code: MMN
Formula: C8H20NO6
Molecular weight: 226.248 g/mol
DrugBank ID: DB02787
Buried Surface Area:61.64 %
Polar Surface area: 137.99 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 7
Rings: 0
Aromatic rings: 0
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 1
Rotatable Bonds: 7

Mass center Coordinates

XYZ
95.1717-24.450550.5903


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
C5CD1ILE- 284.140Hydrophobic
O3NE2GLN- 552.93166.68H-Bond
(Protein Donor)
O5ND2ASN- 743.14156.08H-Bond
(Protein Donor)
O6OD1ASN- 743.24162.73H-Bond
(Ligand Donor)
C6CD1ILE- 793.790Hydrophobic
C6CEMET- 833.980Hydrophobic
C8CEMET- 1574.340Hydrophobic
N1OHTYR- 1862.96165.01H-Bond
(Ligand Donor)
O1OHTYR- 1862.86150.84H-Bond
(Protein Donor)
C3CZTYR- 1864.070Hydrophobic
O3OD2ASP- 2472.68158.24H-Bond
(Ligand Donor)
O5OD1ASP- 2472.76149.36H-Bond
(Ligand Donor)
O1MN MN- 10012.550Metal Acceptor