Research workbench
Crystal structure of transketolase in complex with tpp intermediate VIII from pichia stipitis
Analyse Crystal structure of transketolase in complex with tpp intermediate VIII from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XT0
- 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
- T6F, CA
- Pockets
- 4 · best druggability 0.56
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
- T6F · 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}-6-O-phosphono-D-glucitol · ligand · chains A
- CA · Calcium ion · metal · chains A
- PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 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 | 0.56 | 0.77 | 36 | PEG |
| 2 | 82 | 0.51 | 0.84 | 20 | CA, T6F |
| 3 | 101 | 0.37 | 0.74 | 16 | empty |
| 4 | 61 | 0.29 | 0.74 | 15 | empty |
Compared structures
- 5XT0 · Crystal Structure of Transketolase in complex with TPP intermediate VIII from Pichia… · 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 5XT0 · PDBe 5XT0 · UniProt P34736
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