MolNFT v1 · #157596 · protein
TI(III)CITRATE-reduced, nucleotide-free form of the nitrogenase fe- protein from a. vinelandii
6N4J · Nitrogenase iron protein 1: “TI(III)CITRATE-reduced, nucleotide-free form of the nitrogenase fe- protein from a. vinelandii”. X-ray diffraction, 1 ligand (SF4), 6 pockets (best druggability 0.78). MolNFT v1 #157596 on GenesisL1: 3D…
- PDB
- 6N4J
- Type
- protein
- Length
- 575 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrogenase iron protein 1
- EC
- 1.18.6.1
- UniProt
- P00459
- Ligands
- SF4
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrogenase iron protein 1 (EC 1.18.6.1) | protein | 289 | 42% helix, 16% strand | P00459 |
| B | Nitrogenase iron protein 1 (EC 1.18.6.1) | protein | 286 | 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
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 764 | 0.78 | 0.82 | 87 | empty |
| 2 | 105 | 0.53 | 0.83 | 33 | SF4 |
| 3 | 113 | 0.47 | 0.80 | 16 | empty |
| 4 | 85 | 0.47 | 0.82 | 18 | empty |
| 5 | 60 | 0.45 | 0.84 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1654 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 6N4J · Ti(III)citrate-reduced, nucleotide-free form of the nitrogenase Fe-protein from A.… · 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 B 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 6N4J · PDBe 6N4J · UniProt P00459
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