MolNFT v1 · #188989 · protein
Cryoem structure of azotobacter vinelandii nitrogenase complex (1:1 FEP:MOFEP, ATP-bound) during catalytic N2 reduction
7UT8 · Nitrogenase molybdenum-iron protein alpha chain: “Cryoem structure of azotobacter vinelandii nitrogenase complex (1:1 FEP:MOFEP, ATP-bound) during catalytic N2…”. Electron microscopy, 7 ligands (HCA, ICS, CLF), 20 pockets (best…
- PDB
- 7UT8
- Type
- protein
- Length
- 2,538 residues
- Chains
- 6
- 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
- HCA, ICS, CLF, ATP, SF4, FE, MG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Nitrogenase molybdenum-iron protein alpha chain (EC 1.18.6.1) | protein | 476 | 48% helix, 14% strand | P07328 |
| B, D | Nitrogenase molybdenum-iron protein beta chain (EC 1.18.6.1) | protein | 522 | 50% helix, 10% strand | C1DGZ8 |
| E, F | Nitrogenase iron protein gamma chain (EC 1.18.6.1) | protein | 271 | 42% helix, 17% strand | C1DGZ6 |
Ligands and binding sites
- 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
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains E, F
- SF4 · Iron/sulfur cluster · ligand · chains A, B, E, F
- FE · Fe (III) ion · metal · 2 copies · chains B, C, D
- MG · Magnesium ion · metal · 2 copies · chains E, F
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 | 557 | 0.87 | 0.93 | 76 | HCA, ICS |
| 2 | 541 | 0.87 | 0.93 | 65 | HCA, ICS |
| 3 | 1042 | 0.85 | 0.87 | 121 | MG, ATP |
| 4 | 836 | 0.85 | 0.87 | 59 | empty |
| 5 | 945 | 0.80 | 0.82 | 79 | empty |
Interfaces
10 interfaces between chains.
- C–D · 4761 Ų buried · 53 hydrogen bonds · protein-protein
- A–B · 4732 Ų buried · 51 hydrogen bonds · protein-protein
- B–D · 3113 Ų buried · 45 hydrogen bonds · protein-protein
- E–F · 1989 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 1409 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 7UT8 · CryoEM structure of Azotobacter vinelandii nitrogenase complex (1:1 FeP:MoFeP, ATP-bound)… · the same entry in another collection · chain A against A, 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 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 P07328
- Every structure of UniProt C1DGZ8
- Every structure of UniProt C1DGZ6
- Elsewhere: RCSB PDB 7UT8 · PDBe 7UT8 · UniProt P07328 · UniProt C1DGZ8 · UniProt C1DGZ6
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