MolNFT v1 · #127786 · protein
Azotobacter vinelandii vanadium nitrogenase
5N6Y: “Azotobacter vinelandii vanadium nitrogenase”. X-ray diffraction, 5 ligands (HCA, 8P8, CLF). MolNFT v1 #127786 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5N6Y
- Type
- protein
- Length
- 2,097 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- UniProt
- P16855, P16856, P16857
- Ligands
- HCA, 8P8, CLF, MG, CO3
Structure
x-ray diffraction · 4 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | — | protein | 473 | — | P16855 |
| E, B | — | protein | 464 | — | P16856 |
| C | — | protein | 112 | — | P16857 |
| F | — | protein | 111 | — | 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 E, B, 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.
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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