MolNFT v1 · #122125 · protein
Crystal structure of glucose-1-phosphate thymidylyltransferase from burkholderia vietnamiensis in complex with 2 -deoxyuridine-5'- monophosphate and 2'-deoxy-thymidine-B-L-rhamnose
5IFY: “Crystal structure of glucose-1-phosphate thymidylyltransferase from burkholderia vietnamiensis in complex…”. X-ray diffraction, 2 ligands (TRH, UMP), 20 pockets (best druggability 0.77). MolNFT v1 #122125 on GenesisL1: 3D structure…
- PDB
- 5IFY
- Type
- protein
- Length
- 1,753 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose-1-phosphate thymidylyltransferase
- EC
- 2.7.7.24
- UniProt
- A4JC15
- Ligands
- TRH, UMP
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 293 | 39% helix, 22% strand | A4JC15 |
| B | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 293 | 37% helix, 22% strand | A4JC15 |
| C | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 289 | 38% helix, 22% strand | A4JC15 |
| F | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 292 | 36% helix, 22% strand | A4JC15 |
Ligands and binding sites
- TRH · 2'-deoxy-thymidine-beta-L-rhamnose · ligand · 6 copies · chains A, B, C, D, E, F
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 679 | 0.77 | 0.82 | 79 | TRH |
| 2 | 68 | 0.75 | 0.99 | 15 | empty |
| 3 | 67 | 0.74 | 0.98 | 14 | empty |
| 4 | 60 | 0.73 | 0.99 | 14 | empty |
| 5 | 294 | 0.71 | 0.85 | 33 | UMP |
Interfaces
6 interfaces between chains.
- A–B · 1851 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 1732 Ų buried · 36 hydrogen bonds · protein-protein
- E–F · 1515 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1394 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 1295 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5IFY · Crystal structure of Glucose-1-phosphate thymidylyltransferase from Burkholderia… · 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 A4JC15
- Elsewhere: RCSB PDB 5IFY · PDBe 5IFY · UniProt A4JC15
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.