Research workbench
The nitrogenase fe protein from azotobacter vinelandii complexed with mgadp
Analyse The nitrogenase fe protein from azotobacter vinelandii complexed with mgadp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FP6
- Type
- protein
- Length
- 1,148 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrogenase iron protein
- EC
- 1.18.6.1
- UniProt
- P00459
- Ligands
- ADP, SF4, MG
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nitrogenase iron protein (EC 1.18.6.1) | protein | 289 | 41% helix, 16% strand | P00459 |
| C, D | Nitrogenase iron protein (EC 1.18.6.1) | protein | 285 | 40% helix, 17% strand | P00459 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 787 | 0.82 | 0.85 | 79 | MG, ADP |
| 2 | 740 | 0.81 | 0.85 | 74 | MG, ADP |
| 3 | 530 | 0.77 | 0.84 | 49 | MG, ADP |
| 4 | 585 | 0.75 | 0.82 | 52 | MG, ADP |
| 5 | 349 | 0.68 | 0.82 | 47 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2290 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 2228 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 862 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1FP6 · The nitrogenase fe protein from azotobacter vinelandii complexed with mgadp · 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 C against A, TM-score 0.96
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 1FP6 · PDBe 1FP6 · UniProt P00459
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