MolNFT v1 · #188990 · protein
Cryoem structure of azotobacter vinelandii nitrogenase complex (1:1 FEP:MOFEP, ADP/ATP-bound) during catalytic N2 reduction
7UT9 · Nitrogenase molybdenum-iron protein alpha chain: “Cryoem structure of azotobacter vinelandii nitrogenase complex (1:1 FEP:MOFEP, ADP/ATP-bound) during…”. Electron microscopy, 8 ligands (HCA, ICS, CLF), 20 pockets (best druggability…
- PDB
- 7UT9
- 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, ADP, SF4, ATP, FE, MG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 5 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrogenase molybdenum-iron protein alpha chain (EC 1.18.6.1) | protein | 477 | 49% helix, 14% strand | P07328 |
| B, D | Nitrogenase molybdenum-iron protein beta chain (EC 1.18.6.1) | protein | 522 | 52% helix, 11% strand | C1DGZ8 |
| C | Nitrogenase molybdenum-iron protein alpha chain (EC 1.18.6.1) | protein | 475 | 48% helix, 14% strand | P07328 |
| E | Nitrogenase iron protein gamma chain (EC 1.18.6.1) | protein | 271 | 41% helix, 16% strand | C1DGZ6 |
| F | Nitrogenase iron protein gamma chain (EC 1.18.6.1) | protein | 271 | 39% helix, 15% 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
- ADP · Adenosine-5'-diphosphate · ligand · chains E, F
- SF4 · Iron/sulfur cluster · ligand · chains A, B, E, F
- ATP · Adenosine-5'-triphosphate · ligand · chains E, F
- FE · Fe (III) ion · metal · 2 copies · chains B, D, A
- 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 562 | 0.88 | 0.94 | 75 | HCA, ICS |
| 2 | 573 | 0.88 | 0.93 | 74 | HCA, ICS |
| 3 | 914 | 0.86 | 0.87 | 71 | empty |
| 4 | 483 | 0.84 | 0.91 | 63 | MG, ATP |
| 5 | 608 | 0.84 | 0.89 | 80 | MG, ADP |
Interfaces
10 interfaces between chains.
- A–B · 4763 Ų buried · 52 hydrogen bonds · protein-protein
- C–D · 4707 Ų buried · 49 hydrogen bonds · protein-protein
- B–D · 3152 Ų buried · 48 hydrogen bonds · protein-protein
- E–F · 1816 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1412 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 7UT9 · CryoEM structure of Azotobacter vinelandii nitrogenase complex (1:1 FeP:MoFeP… · 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 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 7UT9 · PDBe 7UT9 · UniProt P07328 · UniProt C1DGZ8 · UniProt C1DGZ6
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