MolNFT v1 · #138411 · protein
Structure of a flavodoxin from the domain archaea
5WID: “Structure of a flavodoxin from the domain archaea”. X-ray diffraction, 1 ligand (FMN), 6 pockets (best druggability 0.56). MolNFT v1 #138411 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5WID
- Type
- protein
- Length
- 431 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Flavodoxin
- UniProt
- Q8TPV5
- Ligands
- FMN
- Pockets
- 6 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Flavodoxin | protein | 144 | 45% helix, 26% strand | Q8TPV5 |
| B | Flavodoxin | protein | 143 | 46% helix, 26% strand | Q8TPV5 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 3 copies · chains A, B, C
- ACT · Acetate ion · additive · 2 copies · chains A
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 198 | 0.56 | 0.79 | 28 | FMN |
| 2 | 116 | 0.39 | 0.75 | 23 | empty |
| 3 | 109 | 0.38 | 0.74 | 18 | empty |
| 4 | 61 | 0.34 | 0.77 | 18 | FMN |
| 5 | 54 | 0.33 | 0.77 | 18 | FMN |
Interfaces
2 interfaces between chains.
- A–B · 941 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 276 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5WID · Structure of a flavodoxin from the domain Archaea · the same entry in another collection · chain A against A, TM-score 1.00
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 Q8TPV5
- Elsewhere: RCSB PDB 5WID · PDBe 5WID · UniProt Q8TPV5
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