Research workbench
Transketolase from E. COLI in complex with substrate D-xylulose-5- phosphate
Analyse Transketolase from E. COLI in complex with substrate D-xylulose-5- phosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R8O
- Type
- protein
- Length
- 1,329 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transketolase 1
- EC
- 2.2.1.1
- UniProt
- P27302
- Ligands
- T5X, CA
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transketolase 1 (EC 2.2.1.1) | protein | 662 | 47% helix, 14% strand | P27302 |
| B | Transketolase 1 (EC 2.2.1.1) | protein | 667 | 48% helix, 14% strand | P27302 |
Ligands and binding sites
- T5X · 2-C-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium-2-yl}-5-O-phosphono-D-xylitol · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 338 | 0.75 | 0.86 | 51 | CA, T5X |
| 2 | 338 | 0.75 | 0.86 | 50 | CA, T5X |
| 3 | 347 | 0.57 | 0.76 | 50 | empty |
| 4 | 359 | 0.57 | 0.75 | 49 | empty |
| 5 | 341 | 0.57 | 0.76 | 49 | EDO |
Interfaces
1 interface between chains.
- A–B · 4287 Ų buried · 79 hydrogen bonds · protein-protein
Compared structures
- 2R8O · Transketolase from E. coli in complex with substrate D-xylulose-5-phosphate · the same entry in another collection · chain A against A, TM-score 1.00
- P27302 · AlphaFold monomer V2.0 prediction for transketolase 1 (P27302) · a predicted model of the same protein · 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 P27302
- Elsewhere: RCSB PDB 2R8O · PDBe 2R8O · UniProt P27302
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