MolNFT v1 · #171550 · protein
[4FE-4S]-dependent thiouracil desulfidase tuds (DUF523VCZ) solved by fe-sad phasing
6Z92 · DUF523 domain-containing protein: “[4FE-4S]-dependent thiouracil desulfidase tuds (DUF523VCZ) solved by fe-sad phasing”. X-ray diffraction, 1 ligand (SF4), 3 pockets (best druggability 0.67). MolNFT v1 #171550 on GenesisL1: 3D…
- PDB
- 6Z92
- Type
- protein
- Length
- 301 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DUF523 domain-containing protein
- UniProt
- A0A2H4Z949
- Ligands
- SF4
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DUF523 domain-containing protein | protein | 150 | 37% helix, 20% strand | A0A2H4Z949 |
| B | DUF523 domain-containing protein | protein | 151 | 36% helix, 20% strand | A0A2H4Z949 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains B
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 | 200 | 0.67 | 0.85 | 24 | EDO |
| 2 | 173 | 0.66 | 0.85 | 33 | SF4, EDO, PEG |
| 3 | 168 | 0.62 | 0.84 | 31 | SF4, EDO |
Interfaces
1 interface between chains.
- A–B · 627 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6Z92 · [4Fe-4S]-dependent thiouracil desulfidase TudS (DUF523Vcz) solved by Fe-SAD phasing · 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 6Z92 · PDBe 6Z92 · UniProt A0A2H4Z949
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