Research workbench
Crystal structure of a glucose-1-phosphate thymidylyltransferase from burkholderia vietnamiensis
Analyse Crystal structure of a glucose-1-phosphate thymidylyltransferase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IDS
- Type
- protein
- Length
- 1,152 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
- A4JIV2
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 289 | 38% helix, 23% strand | A4JIV2 |
| B | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 288 | 40% helix, 24% strand | A4JIV2 |
| C | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 286 | 38% helix, 23% strand | A4JIV2 |
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 112 | 0.80 | 0.98 | 23 | empty |
| 2 | 59 | 0.73 | 0.98 | 14 | empty |
| 3 | 882 | 0.73 | 0.77 | 88 | empty |
| 4 | 512 | 0.68 | 0.79 | 47 | empty |
| 5 | 339 | 0.59 | 0.76 | 47 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1292 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1202 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 427 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 193 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5IDS · Crystal Structure of a 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 A4JIV2
- Elsewhere: RCSB PDB 5IDS · PDBe 5IDS · UniProt A4JIV2
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