Research workbench
Hybrid cluster protein from desulfovibrio desulfuricans X-ray structure at 1.25A resolution using synchrotron radiation at a wavelength of 0.933A
Analyse Hybrid cluster protein from desulfovibrio desulfuricans X-ray structure at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GNL
- Type
- protein
- Length
- 1,086 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hybrid cluster protein
- UniProt
- Q01770
- Ligands
- SF4, FSO
- Pockets
- 10 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hybrid cluster protein | protein | 543 | 51% helix, 11% strand | Q01770 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- FSO · Iron/sulfur/oxygen hybrid cluster · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.65 | 0.90 | 31 | empty |
| 2 | 69 | 0.62 | 0.90 | 27 | empty |
| 3 | 59 | 0.60 | 0.90 | 22 | empty |
| 4 | 115 | 0.47 | 0.79 | 20 | empty |
| 5 | 88 | 0.45 | 0.80 | 19 | empty |
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1GNL · Hybrid Cluster Protein from Desulfovibrio desulfuricans X-ray structure at 1.25A… · 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 1GNL · PDBe 1GNL · UniProt Q01770
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