Research workbench
Azotobacter vinelandii vanadium nitrogenase
Analyse Azotobacter vinelandii vanadium nitrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5N6Y
- Type
- protein
- Length
- 2,097 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrogenase vanadium-iron protein alpha chain; Nitrogenase vanadium-iron protein beta…
- EC
- 1.18.6.1
- UniProt
- P16855, P16856, P16857
- Ligands
- HCA, 8P8, CLF, MG, CO3
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Nitrogenase vanadium-iron protein alpha chain (EC 1.18.6.1) | protein | 473 | 48% helix, 15% strand | P16855 |
| E, B | Nitrogenase vanadium-iron protein beta chain (EC 1.18.6.1) | protein | 464 | 50% helix, 14% strand | P16856 |
| C | Nitrogenase vanadium-iron protein delta chain (EC 1.18.6.1) | protein | 112 | 72% helix, 0% strand | P16857 |
| F | Nitrogenase vanadium-iron protein delta chain (EC 1.18.6.1) | protein | 111 | 71% helix, 0% strand | P16857 |
Ligands and binding sites
- HCA · 3-hydroxy-3-carboxy-adipic acid · ligand · 2 copies · chains A, B, E, D
- 8P8 · C Fe7 S8 V · ligand · 2 copies · chains A, D
- CLF · FE(8)-S(7) cluster · ligand · 2 copies · chains A, B, E, D
- MG · Magnesium ion · metal · 4 copies · chains A, E, B, D, C, F
- CO3 · Carbonate ion · 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 | 384 | 0.86 | 0.94 | 49 | HCA, 8P8, CO3 |
| 2 | 381 | 0.86 | 0.94 | 51 | HCA, 8P8, CO3 |
| 3 | 1191 | 0.84 | 0.85 | 85 | empty |
| 4 | 69 | 0.75 | 0.99 | 28 | CLF |
| 5 | 65 | 0.74 | 0.99 | 25 | CLF |
Interfaces
7 interfaces between chains.
- A–B · 3359 Ų buried · 52 hydrogen bonds · protein-protein
- E–D · 3354 Ų buried · 49 hydrogen bonds · protein-protein
- E–B · 2342 Ų buried · 41 hydrogen bonds · protein-protein
- A–C · 1768 Ų buried · 29 hydrogen bonds · protein-protein
- D–B · 1744 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 5N6Y · Azotobacter vinelandii vanadium nitrogenase · the same entry in another collection · chain D against D, TM-score 1.00
- P16856 · AlphaFold monomer V2.0 prediction for nitrogenase vanadium-iron protein beta chain… · a predicted model of the same protein · chain E against A, TM-score 0.99
- P16855 · AlphaFold monomer V2.0 prediction for nitrogenase vanadium-iron protein alpha chain… · a predicted model of the same protein · chain A against A, TM-score 0.99
- P16857 · AlphaFold monomer V2.0 prediction for nitrogenase vanadium-iron protein delta chain… · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P16855
- Every structure of UniProt P16856
- Every structure of UniProt P16857
- Elsewhere: RCSB PDB 5N6Y · PDBe 5N6Y · UniProt P16855 · UniProt P16856 · UniProt P16857
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