MolNFT v1 · #24280 · protein
The crystal structure of the hybrid cluster protein from desulfovibrio desulfuricans containing molecules in the oxidized and reduced states.
1UPX · Hydroxylamine reductase: “The crystal structure of the hybrid cluster protein from desulfovibrio desulfuricans containing molecules in…”. X-ray diffraction, 3 ligands (SF4, SF3, FSO), 9 pockets (best druggability 0.79). MolNFT v1…
- PDB
- 1UPX
- Type
- protein
- Length
- 1,086 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydroxylamine reductase
- UniProt
- Q01770
- Ligands
- SF4, SF3, FSO
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hydroxylamine reductase | protein | 543 | 51% helix, 11% strand | Q01770 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- SF3 · FE4-S3 cluster · ligand · 2 copies · chains A, B
- FSO · Iron/sulfur/oxygen hybrid cluster · ligand · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 123 | 0.79 | 0.96 | 52 | empty |
| 2 | 55 | 0.67 | 0.94 | 28 | empty |
| 3 | 109 | 0.45 | 0.78 | 20 | empty |
| 4 | 88 | 0.45 | 0.80 | 16 | empty |
| 5 | 83 | 0.42 | 0.79 | 21 | empty |
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 1UPX · The crystal structure of the Hybrid Cluster Protein from Desulfovibrio desulfuricans… · the same entry in another collection · chain A against A, TM-score 1.00
- Q01770 · AlphaFold monomer V2.0 prediction for hydroxylamine reductase (Q01770) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 Q01770
- Elsewhere: RCSB PDB 1UPX · PDBe 1UPX · UniProt Q01770
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