MolNFT v1 · #63338 · protein
Desulfovibrio desulfuricans (atcc 29577) oxidized flavodoxin alternate conformers
3F6S: “Desulfovibrio desulfuricans (atcc 29577) oxidized flavodoxin alternate conformers”. X-ray diffraction, 1 ligand (FMN), 10 pockets (best druggability 0.66). MolNFT v1 #63338 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3F6S
- Type
- protein
- Length
- 1,176 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Flavodoxin
- UniProt
- P26492
- Ligands
- FMN
- Pockets
- 10 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F, H, I, G | Flavodoxin | protein | 147 | 35% helix, 24% strand | P26492 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 8 copies · chains A, G, B, D, E, F, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 549 | 0.66 | 0.77 | 61 | FMN |
| 2 | 517 | 0.66 | 0.78 | 56 | FMN |
| 3 | 433 | 0.66 | 0.79 | 55 | FMN |
| 4 | 292 | 0.54 | 0.76 | 30 | empty |
| 5 | 214 | 0.47 | 0.74 | 30 | empty |
Interfaces
5 interfaces between chains.
- D–E · 621 Ų buried · 9 hydrogen bonds · protein-protein
- A–F · 550 Ų buried · 15 hydrogen bonds · protein-protein
- A–G · 376 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 373 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 370 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3F6S · Desulfovibrio desulfuricans (ATCC 29577) oxidized flavodoxin alternate conformers · the same entry in another collection · chain G against G, TM-score 1.00
- P26492 · AlphaFold monomer V2.0 prediction for flavodoxin (P26492) · a predicted model of the same protein · chain I against A, TM-score 0.99
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 P26492
- Elsewhere: RCSB PDB 3F6S · PDBe 3F6S · UniProt P26492
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