Research workbench
A. vinelandii vanadium nitrogenase, turnover state
Analyse A. vinelandii vanadium nitrogenase, turnover state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FEA
- Type
- protein
- Length
- 2,074 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrogenase protein alpha chain; Vanadium nitrogenase beta subunit, vnfk; Vanadium…
- EC
- 1.18.6.1
- UniProt
- C1DI25, C1DI23, C1DI24
- Ligands
- HCA, D6N, CLF, MG, ZN, CO3, H2S
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Nitrogenase protein alpha chain (EC 1.18.6.1) | protein | 461 | 50% helix, 15% strand | C1DI25 |
| B, E | Vanadium nitrogenase beta subunit, vnfk (EC 1.18.6.1) | protein | 464 | 50% helix, 14% strand | C1DI23 |
| C | Vanadium nitrogenase, delta subunit, vnfg (EC 1.18.6.1) | protein | 113 | 73% helix, 0% strand | C1DI24 |
| F | Vanadium nitrogenase, delta subunit, vnfg (EC 1.18.6.1) | protein | 111 | 69% helix, 0% strand | C1DI24 |
Ligands and binding sites
- HCA · 3-hydroxy-3-carboxy-adipic acid · ligand · 2 copies · chains A, B, D, E
- D6N · FeV · ligand · 2 copies · chains A, D
- CLF · FE(8)-S(7) cluster · ligand · 2 copies · chains A, B, D, E
- MG · Magnesium ion · metal · 4 copies · chains A, B, E, D, C, F
- ZN · Zinc ion · metal · 2 copies · chains A, E, B, D
- CO3 · Carbonate ion · ion · 2 copies · chains A, D
- H2S · Hydrosulfuric acid · ion · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 404 | 0.86 | 0.94 | 55 | HCA, D6N, CO3 |
| 2 | 405 | 0.86 | 0.94 | 55 | D6N, HCA, CO3 |
| 3 | 1179 | 0.85 | 0.85 | 87 | empty |
| 4 | 69 | 0.75 | 0.99 | 26 | CLF |
| 5 | 66 | 0.74 | 0.98 | 24 | CLF |
Interfaces
7 interfaces between chains.
- A–B · 3360 Ų buried · 53 hydrogen bonds · protein-protein
- D–E · 3343 Ų buried · 51 hydrogen bonds · protein-protein
- B–E · 2327 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 1764 Ų buried · 31 hydrogen bonds · protein-protein
- D–F · 1714 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 6FEA · A. vinelandii vanadium nitrogenase, turnover state · 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 C1DI25
- Every structure of UniProt C1DI23
- Every structure of UniProt C1DI24
- Elsewhere: RCSB PDB 6FEA · PDBe 6FEA · UniProt C1DI25 · UniProt C1DI23 · UniProt C1DI24
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