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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:

2w5u

2.620 Å

X-ray

2008-12-12

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Flavodoxin
ID:FLAV_HELPY
AC:O25776
Organism:Helicobacter pylori
Reign:Bacteria
TaxID:85962
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:23.667
Number of residues:29
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.088327.375

% Hydrophobic% Polar
47.4252.58
According to VolSite

Ligand :
2w5u_1 Structure
HET Code: FMN
Formula: C17H19N4O9P
Molecular weight: 454.328 g/mol
DrugBank ID: DB03247
Buried Surface Area:63.73 %
Polar Surface area: 217.05 Å2
Number of
H-Bond Acceptors: 12
H-Bond Donors: 4
Rings: 3
Aromatic rings: 1
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 7

Mass center Coordinates

XYZ
3.83055-0.86558165.0511


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
O3POG1THR- 102.59153.82H-Bond
(Protein Donor)
O2PNASP- 112.6136.88H-Bond
(Protein Donor)
O1PNSER- 123.29122.76H-Bond
(Protein Donor)
O4'ND2ASN- 143.12157.93H-Bond
(Protein Donor)
O1PNASN- 142.8152.8H-Bond
(Protein Donor)
C5'CBASN- 144.320Hydrophobic
O3PNALA- 152.84166.43H-Bond
(Protein Donor)
C4'CBPRO- 533.90Hydrophobic
O2'OTHR- 542.53149.08H-Bond
(Ligand Donor)
O2'NTHR- 542.93144.7H-Bond
(Protein Donor)
C4'CBLEU- 864.290Hydrophobic
N1NASP- 883.09163.01H-Bond
(Protein Donor)
O2NASP- 883.11131.23H-Bond
(Protein Donor)
C1'CBASP- 8840Hydrophobic
C1'CE2TYR- 924.340Hydrophobic
O2NALA- 972.84167.14H-Bond
(Protein Donor)
O3'OD2ASP- 1422.74179.24H-Bond
(Ligand Donor)