Research workbench
The crystal structure of the hybrid cluster protein from desulfovibrio desulfuricans containing molecules in the oxidized and reduced states.
Analyse The crystal structure of the hybrid cluster protein from desulfovibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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