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Asymmetric nucleotide binding in the nitrogenase complex
Analyse Asymmetric nucleotide binding in the nitrogenase complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WZA
- Type
- protein
- Length
- 3,092 residues
- Chains
- 8
- Method
- x-ray diffraction
- 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, P07329, P00459
- Ligands
- HCA, ICS, CLF, SF4, ADP, ACP, MG, FE
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Nitrogenase molybdenum-iron protein alpha chain (EC 1.18.6.1) | protein | 477 | 47% helix, 15% strand | P07328 |
| B, D | Nitrogenase molybdenum-iron protein beta chain (EC 1.18.6.1) | protein | 522 | 53% helix, 10% strand | P07329 |
| E, G | Nitrogenase iron protein 1 (EC 1.18.6.1) | protein | 276 | 45% helix, 17% strand | P00459 |
| F, H | Nitrogenase iron protein 1 (EC 1.18.6.1) | protein | 271 | 45% helix, 17% strand | P00459 |
Ligands and binding sites
- HCA · 3-hydroxy-3-carboxy-adipic acid · ligand · 2 copies · chains A, C
- 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
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains E, F, G, H
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 2 copies · chains E, F, G, H
- MG · Magnesium ion · metal · 4 copies · chains E, F, G, H
- FE · Fe (III) ion · metal · 2 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 541 | 0.88 | 0.95 | 74 | HCA, ICS |
| 2 | 524 | 0.88 | 0.94 | 67 | HCA, ICS |
| 3 | 888 | 0.85 | 0.87 | 68 | empty |
| 4 | 1071 | 0.82 | 0.83 | 85 | empty |
| 5 | 1003 | 0.82 | 0.83 | 81 | empty |
Interfaces
15 interfaces between chains.
- A–B · 4765 Ų buried · 60 hydrogen bonds · protein-protein
- C–D · 4736 Ų buried · 59 hydrogen bonds · protein-protein
- B–D · 3157 Ų buried · 68 hydrogen bonds · protein-protein
- E–F · 1930 Ų buried · 27 hydrogen bonds · protein-protein
- G–H · 1778 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 4WZA · Asymmetric Nucleotide Binding in the Nitrogenase Complex · the same entry in another collection · chain H against H, 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
- 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
- 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 0.98
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 P07328
- Every structure of UniProt P07329
- Every structure of UniProt P00459
- Elsewhere: RCSB PDB 4WZA · PDBe 4WZA · UniProt P07328 · UniProt P07329 · UniProt P00459
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