MolNFT v1 · #4130 · protein
Modulating the midpoint potential of the [4FE-4S] cluster of the nitrogenase fe protein
1DE0 · Nitrogenase iron protein: “Modulating the midpoint potential of the [4FE-4S] cluster of the nitrogenase fe protein”. X-ray diffraction, 1 ligand (SF4), 3 pockets (best druggability 0.75). MolNFT v1 #4130 on GenesisL1: 3D structure…
- PDB
- 1DE0
- Type
- protein
- Length
- 578 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
- 3 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, 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
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 576 | 0.75 | 0.82 | 82 | SF4 |
| 2 | 443 | 0.70 | 0.81 | 59 | empty |
| 3 | 81 | 0.44 | 0.81 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1823 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 1DE0 · Modulating the midpoint potential of the [4FE-4S] cluster of the nitrogenase fe protein · the same entry in another collection · chain B against B, 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 0.94
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 1DE0 · PDBe 1DE0 · UniProt P00459
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