MolNFT v1 · #52606 · protein
Flavodoxin from helicobacter pylori in complex with the C3 inhibitor
2W5U: “Flavodoxin from helicobacter pylori in complex with the C3 inhibitor”. X-ray diffraction, 2 ligands (FMN, IC3), 4 pockets (best druggability 0.43). MolNFT v1 #52606 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2W5U
- Type
- protein
- Length
- 326 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Flavodoxin
- UniProt
- O25776
- Ligands
- FMN, IC3
- Pockets
- 4 · best druggability 0.43
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Flavodoxin | protein | 163 | 40% helix, 23% strand | O25776 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- IC3 · [2-(5-amino-4-cyano-1H-pyrazol-1-yl)-5-(trifluoromethyl)phenyl](hydroxy)oxoammonium · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.43 | 0.79 | 24 | FMN |
| 2 | 91 | 0.41 | 0.78 | 23 | FMN, IC3 |
| 3 | 62 | 0.32 | 0.76 | 13 | empty |
| 4 | 61 | 0.30 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 288 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O25776
- Elsewhere: RCSB PDB 2W5U · PDBe 2W5U · UniProt O25776
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