Research workbench
Specificity of coenzyme binding in thiamin diphosphate dependent enzymes: crystal structures of yeast transketolase in complex with analogs of thiamin diphosphate
Analyse Specificity of coenzyme binding in thiamin diphosphate dependent enzymes… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TKA
- Type
- protein
- Length
- 1,356 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transketolase
- EC
- 2.2.1.1
- UniProt
- P23254
- Ligands
- N3T, CA
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Transketolase (EC 2.2.1.1) | protein | 678 | 44% helix, 13% strand | P23254 |
Ligands and binding sites
- N3T · 3'-deazo-thiamin diphosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 929 | 0.80 | 0.82 | 85 | empty |
| 2 | 376 | 0.76 | 0.86 | 50 | CA, N3T |
| 3 | 398 | 0.75 | 0.85 | 49 | CA, N3T |
| 4 | 344 | 0.63 | 0.79 | 46 | empty |
| 5 | 280 | 0.54 | 0.76 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 4583 Ų buried · 81 hydrogen bonds · protein-protein
Compared structures
- 1TKA · Specificity of coenzyme binding in thiamin diphosphate dependent enzymes: crystal… · the same entry in another collection · chain A against A, TM-score 1.00
- P23254 · AlphaFold monomer V2.0 prediction for transketolase 1 (P23254) · 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 P23254
- Elsewhere: RCSB PDB 1TKA · PDBe 1TKA · UniProt P23254
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