MolNFT v1 · #122051 · protein
Crystal structure of a glucose-1-phosphate thymidylyltransferase from burkholderia vietnamiensis with bound thymidine
5IDT: “Crystal structure of a glucose-1-phosphate thymidylyltransferase from burkholderia vietnamiensis with bound…”. X-ray diffraction, 1 ligand (THM), 20 pockets (best druggability 0.77). MolNFT v1 #122051 on GenesisL1: 3D structure…
- PDB
- 5IDT
- Type
- protein
- Length
- 1,153 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
- Ligands
- THM
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 289 | 39% helix, 23% strand | A4JIV2 |
| C | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 286 | 39% helix, 23% strand | A4JIV2 |
Ligands and binding sites
- THM · Thymidine · ligand · 2 copies · chains A, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 80 | 0.77 | 0.99 | 19 | empty |
| 2 | 57 | 0.73 | 0.99 | 14 | empty |
| 3 | 900 | 0.73 | 0.77 | 88 | empty |
| 4 | 405 | 0.66 | 0.79 | 43 | THM |
| 5 | 384 | 0.58 | 0.75 | 41 | THM |
Interfaces
4 interfaces between chains.
- C–D · 1232 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1196 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 418 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 195 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5IDT · 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 5IDT · PDBe 5IDT · UniProt A4JIV2
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