MolNFT v1 · #15897 · protein
Crystallographic structure of the nitrogenase iron protein from azotobacter vinelandii
1NIP: “Crystallographic structure of the nitrogenase iron protein from azotobacter vinelandii”. X-ray diffraction, 3 ligands (SF4, ADP, MG), 2 pockets (best druggability 0.78). MolNFT v1 #15897 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1NIP
- Type
- protein
- Length
- 570 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrogenase iron protein
- UniProt
- P00459
- Ligands
- SF4, ADP, MG
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrogenase iron protein | protein | 283 | 39% helix, 15% strand | P00459 |
| B | Nitrogenase iron protein | protein | 287 | 43% helix, 13% strand | P00459 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1067 | 0.78 | 0.80 | 130 | MG, ADP |
| 2 | 73 | 0.48 | 0.83 | 26 | SF4 |
Interfaces
1 interface between chains.
- A–B · 1448 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1NIP · Crystallographic structure of the 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 1NIP · PDBe 1NIP · UniProt P00459
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