MolNFT v1 · #171553 · protein
[4FE-4S]-dependent thiouracil desulfidase tuds (DUF523VCZ) soaked with 4-thiouracil (12.65 kev, 7.125 kev (fe-sad) and 6.5 kev (S-sad) data)
6Z96: “[4FE-4S]-dependent thiouracil desulfidase tuds (DUF523VCZ) soaked with 4-thiouracil (12.65 kev, 7.125 kev…”. X-ray diffraction, 2 ligands (SF4, H2S), 3 pockets (best druggability 0.65). MolNFT v1 #171553 on GenesisL1: 3D structure…
- PDB
- 6Z96
- Type
- protein
- Length
- 306 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tuds
- 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 | Tuds | protein | 155 | 34% helix, 19% strand | A0A2H4Z949 |
| B | Tuds | 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 · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, 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 | 154 | 0.65 | 0.86 | 30 | SF4, H2S, EDO |
| 2 | 157 | 0.65 | 0.86 | 32 | SF4, H2S, EDO |
| 3 | 189 | 0.64 | 0.84 | 22 | EDO |
Interfaces
1 interface between chains.
- A–B · 619 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6Z96 · [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 6Z96 · PDBe 6Z96 · UniProt A0A2H4Z949
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