Research workbench
Nitrogenase complex from azotobacter vinelandii stabilized by ADP- tetrafluoroaluminate
Analyse Nitrogenase complex from azotobacter vinelandii stabilized by ADP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1N2C
- Type
- protein
- Length
- 3,096 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrogenase molybdenum-iron protein; Nitrogenase iron protein
- EC
- 1.18.6.1
- UniProt
- P07328, P07329, P00459
- Ligands
- ALF, ADP, HCA, CFM, CLF, SF4, MG, CA
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Nitrogenase molybdenum-iron protein (EC 1.18.6.1) | protein | 478 | 49% helix, 13% strand | P07328 |
| B, D | Nitrogenase molybdenum-iron protein (EC 1.18.6.1) | protein | 522 | 54% helix, 10% strand | P07329 |
| E, F, G, H | Nitrogenase iron protein (EC 1.18.6.1) | protein | 274 | 46% helix, 17% strand | P00459 |
Ligands and binding sites
- ALF · Tetrafluoroaluminate ion · ligand · 4 copies · chains E, F, G, H
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains E, F, G, H
- HCA · 3-hydroxy-3-carboxy-adipic acid · ligand · 2 copies · chains A, C, D
- CFM · Fe-Mo-S cluster · 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
- CA · Calcium ion · metal · 2 copies · chains B, C, D, A
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 | 525 | 0.88 | 0.95 | 75 | HCA, CFM |
| 2 | 907 | 0.86 | 0.88 | 64 | empty |
| 3 | 425 | 0.86 | 0.94 | 48 | HCA, CFM |
| 4 | 149 | 0.81 | 0.98 | 47 | ALF, ADP |
| 5 | 151 | 0.80 | 0.97 | 48 | ALF, ADP |
Interfaces
15 interfaces between chains.
- A–B · 4705 Ų buried · 61 hydrogen bonds · protein-protein
- C–D · 4700 Ų buried · 62 hydrogen bonds · protein-protein
- B–D · 3102 Ų buried · 62 hydrogen bonds · protein-protein
- G–H · 2603 Ų buried · 29 hydrogen bonds · protein-protein
- E–F · 2586 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 1N2C · Nitrogenase complex from azotobacter vinelandii stabilized by ADP-tetrafluoroaluminate · the same entry in another collection · chain H against H, TM-score 1.00
- P07329 · AlphaFold monomer V2.0 prediction for nitrogenase molybdenum-iron protein beta chain… · a predicted model of the same protein · chain B 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
- P00459 · AlphaFold monomer V2.0 prediction for nitrogenase iron protein 1 (P00459) · a predicted model of the same protein · chain E against A, TM-score 0.97
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 P07329
- Every structure of UniProt P00459
- Elsewhere: RCSB PDB 1N2C · PDBe 1N2C · UniProt P07328 · UniProt P07329 · UniProt P00459
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