Research workbench
Thymidylyltransferase complexed with thymidylyldiphosphate-glucose
Analyse Thymidylyltransferase complexed with thymidylyldiphosphate-glucose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1H5T
- Type
- protein
- Length
- 1,160 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose-1-phosphate thymidylyltransferase 1
- EC
- 2.7.7.24
- UniProt
- P37744
- Ligands
- TYD, DAU, SO4
- Pockets
- 18 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Glucose-1-phosphate thymidylyltransferase 1 (EC 2.7.7.24) | protein | 290 | 38% helix, 23% strand | P37744 |
| B | Glucose-1-phosphate thymidylyltransferase 1 (EC 2.7.7.24) | protein | 290 | 39% helix, 23% strand | P37744 |
Ligands and binding sites
- TYD · Thymidine-5'-diphosphate · ligand · 4 copies · chains A, D, B, C
- DAU · 2'deoxy-thymidine-5'-diphospho-alpha-D-glucose · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 609 | 0.78 | 0.84 | 66 | DAU |
| 2 | 74 | 0.76 | 0.99 | 17 | empty |
| 3 | 622 | 0.75 | 0.82 | 64 | DAU |
| 4 | 65 | 0.75 | 0.99 | 17 | empty |
| 5 | 563 | 0.75 | 0.82 | 57 | DAU |
Interfaces
6 interfaces between chains.
- B–C · 1465 Ų buried · 35 hydrogen bonds · protein-protein
- A–D · 1446 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 1418 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1402 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 41 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1H5T · Thymidylyltransferase complexed with Thymidylyldiphosphate-glucose · the same entry in another collection · chain A against A, TM-score 1.00
- P37744 · AlphaFold monomer V2.0 prediction for glucose-1-phosphate thymidylyltransferase 1 (P37744) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P37744
- Elsewhere: RCSB PDB 1H5T · PDBe 1H5T · UniProt P37744
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