MolNFT v1 · #188991 · protein
Cryoem structure of azotobacter vinelandii nitrogenase complex (2:1 FEP:MOFEP) inhibited by befx during catalytic N2 reduction
7UTA · Nitrogenase molybdenum-iron protein alpha chain: “Cryoem structure of azotobacter vinelandii nitrogenase complex (2:1 FEP:MOFEP) inhibited by befx during…”. Electron microscopy, 8 ligands (ADP, HCA, ICS), 20 pockets (best…
- PDB
- 7UTA
- Type
- protein
- Length
- 3,068 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrogenase molybdenum-iron protein alpha chain; Nitrogenase molybdenum-iron protein beta…
- EC
- 1.18.6.1
- UniProt
- P07328, C1DGZ8, C1DGZ6
- Ligands
- ADP, HCA, ICS, CLF, SF4, MG, 0BE, FE
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 5 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrogenase molybdenum-iron protein alpha chain (EC 1.18.6.1) | protein | 470 | 49% helix, 15% strand | P07328 |
| B, D | Nitrogenase molybdenum-iron protein beta chain (EC 1.18.6.1) | protein | 522 | 51% helix, 11% strand | C1DGZ8 |
| C | Nitrogenase molybdenum-iron protein alpha chain (EC 1.18.6.1) | protein | 472 | 48% helix, 14% strand | P07328 |
| E, H | Nitrogenase iron protein gamma chain (EC 1.18.6.1) | protein | 270 | 43% helix, 17% strand | C1DGZ6 |
| F, G | Nitrogenase iron protein gamma chain (EC 1.18.6.1) | protein | 271 | 43% helix, 13% strand | C1DGZ6 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains E, F, G, H
- HCA · 3-hydroxy-3-carboxy-adipic acid · ligand · 2 copies · chains A, B, C, D
- ICS · iron-sulfur-molybdenum cluster with interstitial carbon · ligand · 2 copies · chains A, C
- CLF · FE(8)-S(7) cluster · ligand · 2 copies · chains A, B, C, D
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B, E, F, C, D, G, H
- MG · Magnesium ion · metal · 4 copies · chains E, F, G, H
- 0BE · Beryllium · metal · 4 copies · chains E, F, G, H
- FE · Fe (III) ion · metal · 2 copies · chains B, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 561 | 0.88 | 0.94 | 74 | HCA, ICS |
| 2 | 529 | 0.88 | 0.94 | 74 | HCA, ICS |
| 3 | 921 | 0.85 | 0.87 | 69 | empty |
| 4 | 265 | 0.82 | 0.94 | 50 | MG, ADP, 0BE |
| 5 | 273 | 0.82 | 0.93 | 54 | MG, ADP, 0BE |
Interfaces
15 interfaces between chains.
- A–B · 4761 Ų buried · 54 hydrogen bonds · protein-protein
- C–D · 4745 Ų buried · 52 hydrogen bonds · protein-protein
- B–D · 3104 Ų buried · 58 hydrogen bonds · protein-protein
- E–F · 2372 Ų buried · 29 hydrogen bonds · protein-protein
- G–H · 2350 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 7UTA · CryoEM structure of Azotobacter vinelandii nitrogenase complex (2:1 FeP:MoFeP) inhibited… · the same entry in another collection · chain F against F, TM-score 1.00
- P07328 · AlphaFold monomer V2.0 prediction for nitrogenase molybdenum-iron protein alpha chain… · a predicted model of the same protein · chain C 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 P07328
- Every structure of UniProt C1DGZ8
- Every structure of UniProt C1DGZ6
- Elsewhere: RCSB PDB 7UTA · PDBe 7UTA · UniProt P07328 · UniProt C1DGZ8 · UniProt C1DGZ6
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