Research workbench
U34-tRNA thiolase ncsa from methanococcus maripaludis with its [4FE- 4S] cluster
Analyse U34-tRNA thiolase ncsa from methanococcus maripaludis with its [4FE- 4S] cluster in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SCY
- Type
- protein
- Length
- 595 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- [4FE-4S]-dependent U34-arnt thiolase
- UniProt
- Q6LXJ4
- Ligands
- SF4, ZN, SO4
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | [4FE-4S]-dependent U34-arnt thiolase | protein | 297 | 42% helix, 11% strand | Q6LXJ4 |
| B | [4FE-4S]-dependent U34-arnt thiolase | protein | 298 | 44% helix, 10% strand | Q6LXJ4 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 45 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 895 | 0.82 | 0.84 | 81 | SF4, SO4 |
| 2 | 643 | 0.78 | 0.84 | 68 | SO4 |
| 3 | 181 | 0.76 | 0.92 | 29 | SO4 |
| 4 | 267 | 0.68 | 0.83 | 32 | ZN, SO4 |
| 5 | 110 | 0.62 | 0.87 | 24 | SF4 |
Interfaces
1 interface between chains.
- A–B · 1054 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6SCY · U34-tRNA thiolase NcsA from Methanococcus maripaludis with its [4Fe-4S] cluster · 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 Q6LXJ4
- Elsewhere: RCSB PDB 6SCY · PDBe 6SCY · UniProt Q6LXJ4
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