Research workbench
[4FE-4S]-dependent thiouracil desulfidase tuds (DUF523VCZ) soaked with 4-thiouracil (S-sad data)
Analyse [4FE-4S]-dependent thiouracil desulfidase tuds (DUF523VCZ) soaked with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZW9
- Type
- protein
- Length
- 304 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DUF523 domain-containing protein
- UniProt
- A0A2H4Z949
- Ligands
- SF4, H2S
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DUF523 domain-containing protein | protein | 153 | 34% helix, 20% strand | A0A2H4Z949 |
| B | DUF523 domain-containing protein | protein | 151 | 34% helix, 20% strand | A0A2H4Z949 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- H2S · Hydrosulfuric acid · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 161 | 0.65 | 0.86 | 33 | SF4, H2S, PEG |
| 2 | 151 | 0.64 | 0.86 | 29 | SF4, H2S, EDO |
| 3 | 182 | 0.57 | 0.81 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 570 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6ZW9 · [4Fe-4S]-dependent thiouracil desulfidase TudS (DUF523Vcz) soaked with 4-thiouracil… · the same entry in another collection · 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 A0A2H4Z949
- Elsewhere: RCSB PDB 6ZW9 · PDBe 6ZW9 · UniProt A0A2H4Z949
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