Research workbench
All-ferrous nitrogenase iron protein from azotobacter vinelandii
Analyse All-ferrous nitrogenase iron 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
- 1G1M
- Type
- protein
- Length
- 576 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrogenase iron protein
- EC
- 1.18.6.1
- UniProt
- P00459
- Ligands
- SF4
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrogenase iron protein (EC 1.18.6.1) | protein | 287 | 42% helix, 16% strand | P00459 |
| B | Nitrogenase iron protein (EC 1.18.6.1) | protein | 289 | 42% helix, 16% strand | P00459 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 572 | 0.74 | 0.82 | 68 | empty |
| 2 | 361 | 0.67 | 0.81 | 49 | empty |
| 3 | 100 | 0.49 | 0.81 | 25 | empty |
| 4 | 80 | 0.47 | 0.82 | 23 | SF4 |
| 5 | 95 | 0.43 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1784 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 1G1M · All-ferrous nitrogenase iron protein from azotobacter vinelandii · the same entry in another collection · 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 A against A, TM-score 0.95
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 P00459
- Elsewhere: RCSB PDB 1G1M · PDBe 1G1M · UniProt P00459
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