MolNFT v1 · #27223 · protein
Crystal structure of the nitrogenase fe protein ASP129GLU
1XDB · Nitrogenase iron protein 1: “Crystal structure of the nitrogenase fe protein ASP129GLU”. X-ray diffraction, 1 ligand (SF4), 4 pockets (best druggability 0.81). MolNFT v1 #27223 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1XDB
- Type
- protein
- Length
- 578 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
- 4 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nitrogenase iron protein 1 (EC 1.18.6.1) | protein | 289 | 41% helix, 15% 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
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1104 | 0.81 | 0.82 | 109 | empty |
| 2 | 90 | 0.56 | 0.85 | 28 | SF4 |
| 3 | 93 | 0.48 | 0.82 | 18 | empty |
| 4 | 71 | 0.47 | 0.83 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1891 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
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 1XDB · PDBe 1XDB · UniProt P00459
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