Research workbench
Crystal structure of transketolase in complex with TPP_III and fructose-6-phosphate from pichia stipitis
Analyse Crystal structure of transketolase in complex with TPP_III and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XU2
- Type
- protein
- Length
- 675 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transketolase
- EC
- 2.2.1.1
- UniProt
- P34736
- Ligands
- F6R, 8EL, TPP, CA
- Pockets
- 6 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transketolase (EC 2.2.1.1) | protein | 675 | 45% helix, 13% strand | P34736 |
Ligands and binding sites
- F6R · Fructose -6-phosphate · ligand · chains A
- 8EL · 2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-2H-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate · ligand · chains A
- TPP · Thiamine diphosphate · ligand · chains A
- CA · Calcium ion · metal · chains A
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 269 | 0.58 | 0.78 | 46 | empty |
| 2 | 80 | 0.52 | 0.85 | 20 | CA, 8EL, TPP |
| 3 | 110 | 0.39 | 0.75 | 17 | empty |
| 4 | 61 | 0.31 | 0.76 | 14 | empty |
| 5 | 73 | 0.30 | 0.73 | 16 | empty |
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 5XU2 · Crystal Structure of Transketolase in complex with TPP_III and fructose-6-phosphate from… · the same entry in another collection · chain A against A, TM-score 1.00
- P34736 · AlphaFold monomer V2.0 prediction for transketolase (P34736) · 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 P34736
- Elsewhere: RCSB PDB 5XU2 · PDBe 5XU2 · UniProt P34736
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