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Crystal structure of a transketolase from burkholderia pseudomallei bound to tpp, calcium and ribose-5-phosphate
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- PDB
- 3UPT
- Type
- protein
- Length
- 1,337 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transketolase
- EC
- 2.2.1.1
- UniProt
- Q2SZA7
- Ligands
- TPP, RP5, CA, BR
- Pockets
- 16 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transketolase (EC 2.2.1.1) | protein | 671 | 46% helix, 14% strand | Q2SZA7 |
| B | Transketolase (EC 2.2.1.1) | protein | 666 | 46% helix, 14% strand | Q2SZA7 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
- RP5 · 5-O-phosphono-beta-D-ribofuranose · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- BR · Bromide ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 341 | 0.75 | 0.86 | 51 | CA, TPP, RP5 |
| 2 | 354 | 0.75 | 0.86 | 51 | RP5, CA, TPP |
| 3 | 255 | 0.59 | 0.79 | 43 | empty |
| 4 | 259 | 0.55 | 0.77 | 39 | empty |
| 5 | 231 | 0.54 | 0.77 | 41 | empty |
Interfaces
1 interface between chains.
- A–B · 4203 Ų buried · 86 hydrogen bonds · protein-protein
Compared structures
- 3UPT · Crystal structure of a transketolase from Burkholderia pseudomallei bound to TPP, calcium… · 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 Q2SZA7
- Elsewhere: RCSB PDB 3UPT · PDBe 3UPT · UniProt Q2SZA7
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