Research workbench
Nitrogenase mofe protein from azotobacter vinelandii
Analyse Nitrogenase mofe protein from azotobacter vinelandii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1M1N
- Type
- protein
- Length
- 3,996 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
- Ligands
- HCA, CFN, CLF, CA
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Nitrogenase molybdenum-iron protein alpha chain (EC 1.18.6.1) | protein | 477 | 46% helix, 14% strand | P07328 |
| B, D, F, H | Nitrogenase molybdenum-iron protein beta chain (EC 1.18.6.1) | protein | 522 | 53% helix, 11% strand | P07329 |
Ligands and binding sites
- HCA · 3-hydroxy-3-carboxy-adipic acid · ligand · 4 copies · chains A, C, E, G
- CFN · FE(7)-Mo-S(9)-N cluster · ligand · 4 copies · chains A, C, E, G
- CLF · FE(8)-S(7) cluster · ligand · 4 copies · chains A, B, C, D, E, F, G, H
- CA · Calcium ion · metal · 4 copies · chains B, C, D, A, F, G, H, E
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 | 564 | 0.88 | 0.94 | 76 | HCA, CFN |
| 2 | 561 | 0.88 | 0.94 | 77 | HCA, CFN |
| 3 | 568 | 0.88 | 0.94 | 79 | HCA, CFN |
| 4 | 495 | 0.87 | 0.94 | 64 | HCA, CFN |
| 5 | 917 | 0.86 | 0.88 | 69 | empty |
Interfaces
14 interfaces between chains.
- E–F · 4710 Ų buried · 54 hydrogen bonds · protein-protein
- G–H · 4706 Ų buried · 55 hydrogen bonds · protein-protein
- A–B · 4704 Ų buried · 54 hydrogen bonds · protein-protein
- C–D · 4690 Ų buried · 55 hydrogen bonds · protein-protein
- B–D · 3147 Ų buried · 56 hydrogen bonds · protein-protein
Compared structures
- 1M1N · Nitrogenase MoFe protein from Azotobacter vinelandii · 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
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
- Elsewhere: RCSB PDB 1M1N · PDBe 1M1N · UniProt P07328 · UniProt P07329
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