MolNFT v1 · #139795 · protein
Crystal structure of transketolase in complex with xylulose-5- phosphate from pichia stipitis
5XQK: “Crystal structure of transketolase in complex with xylulose-5- phosphate from pichia stipitis”. X-ray diffraction, 2 ligands (T5X, CA), 6 pockets (best druggability 0.60). MolNFT v1 #139795 on GenesisL1: 3D structure, binding sites…
- PDB
- 5XQK
- 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
- T5X, CA
- Pockets
- 6 · best druggability 0.60
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
- 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 · 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
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 | 253 | 0.60 | 0.79 | 41 | empty |
| 2 | 73 | 0.53 | 0.86 | 18 | T5X, CA |
| 3 | 115 | 0.39 | 0.74 | 17 | PEG |
| 4 | 72 | 0.31 | 0.74 | 16 | empty |
| 5 | 62 | 0.30 | 0.75 | 14 | empty |
Compared structures
- 5XQK · Crystal Structure of Transketolase in complex with xylulose-5-phosphate 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 5XQK · PDBe 5XQK · UniProt P34736
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