Research workbench
Structure of a short-chain flavodoxin associated with a non-canonical pdu bacterial microcompartment
Analyse Structure of a short-chain flavodoxin associated with a non-canonical pdu… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VEG
- Type
- protein
- Length
- 445 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Flavodoxin
- UniProt
- Q50EJ1
- Ligands
- FMN, NA, CD
- Pockets
- 2 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Flavodoxin | protein | 148 | 46% helix, 25% strand | Q50EJ1 |
| B | Flavodoxin | protein | 149 | 46% helix, 25% strand | Q50EJ1 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 3 copies · chains A, B, C
- NA · Sodium ion · metal · 6 copies · chains A, B, C
- CD · Cadmium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1090 | 0.83 | 0.84 | 95 | FMN, NA |
| 2 | 111 | 0.46 | 0.79 | 20 | FMN |
Interfaces
3 interfaces between chains.
- B–C · 592 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 568 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 89 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5VEG · Structure of a Short-Chain Flavodoxin Associated with a Non-Canonical PDU Bacterial… · 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 Q50EJ1
- Elsewhere: RCSB PDB 5VEG · PDBe 5VEG · UniProt Q50EJ1
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