MolNFT v1 · #27221 · protein
Crystal structure of the nitrogenase fe protein ASP39ASN with mgadp bound
1XD9 · Nitrogenase iron protein 1: “Crystal structure of the nitrogenase fe protein ASP39ASN with mgadp bound”. X-ray diffraction, 3 ligands (ADP, SF4, MG), 4 pockets (best druggability 0.75). MolNFT v1 #27221 on GenesisL1: 3D structure…
- PDB
- 1XD9
- 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
- ADP, SF4, MG
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nitrogenase iron protein 1 (EC 1.18.6.1) | protein | 289 | 39% helix, 17% strand | P00459 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- SF4 · Iron/sulfur cluster · 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
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 506 | 0.75 | 0.83 | 55 | ADP |
| 2 | 501 | 0.75 | 0.83 | 54 | ADP |
| 3 | 223 | 0.55 | 0.78 | 27 | empty |
| 4 | 163 | 0.54 | 0.80 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 2029 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 1XD9 · Crystal Structure of the Nitrogenase Fe protein Asp39Asn with MgADP bound · 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 1XD9 · PDBe 1XD9 · UniProt P00459
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