Research workbench
Structure of sulfurtransferase
Analyse Structure of sulfurtransferase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZTB
- Type
- protein
- Length
- 1,122 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sulfur carrier protein ttub; TRNA-5-METHYLURIDINE(54) 2-sulfurtransferase
- EC
- 2.8.1.15
- UniProt
- Q72LF4, Q72LF3
- Ligands
- SF4, ATP, ZN, SO4
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Sulfur carrier protein ttub | protein | 65 | 15% helix, 38% strand | Q72LF4 |
| B | TRNA-5-METHYLURIDINE(54) 2-sulfurtransferase (EC 2.8.1.15) | protein | 311 | 49% helix, 12% strand | Q72LF3 |
| D, F | Sulfur carrier protein ttub | protein | 64 | 13% helix, 34% strand | Q72LF4 |
| A | TRNA-5-METHYLURIDINE(54) 2-sulfurtransferase (EC 2.8.1.15) | protein | 307 | 50% helix, 12% strand | Q72LF3 |
| C | TRNA-5-METHYLURIDINE(54) 2-sulfurtransferase (EC 2.8.1.15) | protein | 311 | 48% helix, 12% strand | Q72LF3 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains E, B, D, A, F, C
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains E, B, D, A, F, C
- ZN · Zinc ion · metal · 6 copies · chains B, A, C
- SO4 · Sulfate ion · ion · 7 copies · chains B, C, A
- GOL · Glycerol · additive · chains E, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1049 | 0.82 | 0.83 | 105 | SF4, ATP, SO4 |
| 2 | 1096 | 0.79 | 0.81 | 83 | SF4, ATP, SO4 |
| 3 | 1161 | 0.79 | 0.80 | 86 | SF4, ATP, SO4 |
| 4 | 131 | 0.72 | 0.92 | 30 | empty |
| 5 | 80 | 0.69 | 0.94 | 24 | empty |
Interfaces
5 interfaces between chains.
- B–A · 1268 Ų buried · 8 hydrogen bonds · protein-protein
- D–A · 1173 Ų buried · 19 hydrogen bonds · protein-protein
- F–C · 1169 Ų buried · 13 hydrogen bonds · protein-protein
- E–B · 1162 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 307 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5ZTB · Structure of Sulfurtransferase · the same entry in another collection · chain C against C, TM-score 1.00
- Q72LF3 · AlphaFold monomer V2.0 prediction for tRNA-5-METHYLURIDINE(54) 2-sulfurtransferase… · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q72LF4 · AlphaFold monomer V2.0 prediction for sulfur carrier protein ttub (Q72LF4) · a predicted model of the same protein · chain E against A, TM-score 0.91
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 Q72LF4
- Every structure of UniProt Q72LF3
- Elsewhere: RCSB PDB 5ZTB · PDBe 5ZTB · UniProt Q72LF4 · UniProt Q72LF3
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