MolNFT v1 · #71068 · protein
Crystal structure of transketolase in complex with thiamin diphosphate and calcium ion
3M34: “Crystal structure of transketolase in complex with thiamin diphosphate and calcium ion”. X-ray diffraction, 2 ligands (TPP, CA), 6 pockets (best druggability 0.60). MolNFT v1 #71068 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3M34
- Type
- protein
- Length
- 632 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transketolase
- EC
- 2.2.1.1
- UniProt
- Q0P7Y3
- Ligands
- TPP, CA
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transketolase (EC 2.2.1.1) | protein | 632 | 46% helix, 14% strand | Q0P7Y3 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · chains A
- CA · Calcium ion · metal · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.60 | 0.86 | 23 | CA, TPP |
| 2 | 187 | 0.49 | 0.76 | 20 | empty |
| 3 | 76 | 0.44 | 0.81 | 16 | GOL |
| 4 | 114 | 0.41 | 0.76 | 24 | empty |
| 5 | 127 | 0.39 | 0.74 | 26 | empty |
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 3M34 · Crystal structure of transketolase in complex with thiamin diphosphate and calcium ion · the same entry in another collection · 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 Q0P7Y3
- Elsewhere: RCSB PDB 3M34 · PDBe 3M34 · UniProt Q0P7Y3
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