Research workbench
Thymidylyltransferase complexed with udp-glucose
Analyse Thymidylyltransferase complexed with udp-glucose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IIN
- Type
- protein
- Length
- 1,156 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
- Q9F7K6
- Ligands
- UPG
- Pockets
- 19 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 289 | 38% helix, 23% strand | Q9F7K6 |
Ligands and binding sites
- UPG · Uridine-5'-diphosphate-glucose · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1006 | 0.78 | 0.80 | 82 | UPG |
| 2 | 584 | 0.77 | 0.83 | 67 | empty |
| 3 | 70 | 0.76 | 0.99 | 17 | empty |
| 4 | 725 | 0.75 | 0.81 | 68 | UPG |
| 5 | 599 | 0.75 | 0.82 | 60 | UPG |
Interfaces
4 interfaces between chains.
- B–C · 1468 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1438 Ų buried · 38 hydrogen bonds · protein-protein
- A–D · 1428 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 846 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1IIN · thymidylyltransferase complexed with UDP-glucose · 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 Q9F7K6
- Elsewhere: RCSB PDB 1IIN · PDBe 1IIN · UniProt Q9F7K6
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