Research workbench
Thymidylyltransferase complexed with thimidine and glucose-1-phospate
Analyse Thymidylyltransferase complexed with thimidine and glucose-1-phospate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1H5R
- 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
- EC
- 2.7.7.24
- UniProt
- P37744
- Ligands
- THM, G1P, SO4
- Pockets
- 19 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 290 | 38% helix, 23% strand | P37744 |
| B | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 290 | 40% helix, 22% strand | P37744 |
Ligands and binding sites
- THM · Thymidine · ligand · 8 copies · chains A, D, B, C
- G1P · 1-O-phosphono-alpha-D-glucopyranose · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 5 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 703 | 0.79 | 0.83 | 69 | THM, G1P |
| 2 | 75 | 0.77 | 0.99 | 17 | empty |
| 3 | 76 | 0.77 | 0.99 | 17 | empty |
| 4 | 566 | 0.76 | 0.83 | 58 | THM, G1P |
| 5 | 540 | 0.74 | 0.82 | 42 | THM, G1P |
Interfaces
6 interfaces between chains.
- B–C · 1503 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 1475 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 1456 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 1364 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 43 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1H5R · Thymidylyltransferase complexed with Thimidine and Glucose-1-phospate · 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 1H5R · PDBe 1H5R · UniProt P37744
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