Research workbench
Crystal structure of transketolase in complex with aminopyrimidine and cysteine sulfonic acid adduct from pichia stipitis
Analyse Crystal structure of transketolase in complex with aminopyrimidine and cysteine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XTL
- 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
- P23, 8GF, CA
- Pockets
- 5 · 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
- P23 · Propyl trihydrogen diphosphate · ligand · chains A
- 8GF · 2-methylpyrimidin-4-amine · 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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 276 | 0.60 | 0.79 | 46 | PEG |
| 2 | 79 | 0.54 | 0.86 | 16 | P23, CA |
| 3 | 96 | 0.38 | 0.76 | 17 | empty |
| 4 | 74 | 0.30 | 0.73 | 15 | empty |
| 5 | 50 | 0.29 | 0.76 | 15 | empty |
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, oxidation).
Compared structures
- 5XTL · Crystal Structure of Transketolase in complex with aminopyrimidine and cysteine sulfonic… · 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 5XTL · PDBe 5XTL · UniProt P34736
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