MolNFT v1 · #22919 · protein
Specificity of coenzyme binding in thiamin diphosphate dependent enzymes: crystal structures of yeast transketolase in complex with analogs of thiamin diphosphate
1TKC: “Specificity of coenzyme binding in thiamin diphosphate dependent enzymes: crystal structures of yeast…”. X-ray diffraction, 2 ligands (M6T, CA), 13 pockets (best druggability 0.81). MolNFT v1 #22919 on GenesisL1: 3D structure…
- PDB
- 1TKC
- 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
- M6T, CA
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Transketolase (EC 2.2.1.1) | protein | 678 | 46% helix, 13% strand | P23254 |
Ligands and binding sites
- M6T · 6'-methyl-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 | 1006 | 0.81 | 0.82 | 89 | empty |
| 2 | 352 | 0.75 | 0.86 | 49 | CA, M6T |
| 3 | 394 | 0.74 | 0.84 | 50 | M6T |
| 4 | 327 | 0.58 | 0.77 | 40 | empty |
| 5 | 255 | 0.53 | 0.76 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 4578 Ų buried · 77 hydrogen bonds · protein-protein
Compared structures
- 1TKC · 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 1TKC · PDBe 1TKC · UniProt P23254
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