MolNFT v1 · #98061 · protein
Human transketolase in covalent complex with donor ketose D-xylulose- 5-phosphate, crystal 2
4KXW: “Human transketolase in covalent complex with donor ketose D-xylulose- 5-phosphate, crystal 2”. X-ray diffraction, 4 ligands (DX5, TPP, MG), 6 pockets (best druggability 0.47). MolNFT v1 #98061 on GenesisL1: 3D structure, binding…
- PDB
- 4KXW
- Type
- protein
- Length
- 621 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transketolase
- EC
- 2.2.1.1
- UniProt
- P29401
- Ligands
- DX5, TPP, MG, NA
- Pockets
- 6 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transketolase (EC 2.2.1.1) | protein | 621 | 41% helix, 17% strand | P29401 |
Ligands and binding sites
- DX5 · D-xylitol-5-phosphate · ligand · 2 copies · chains A
- TPP · Thiamine diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- NA · Sodium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 12 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.47 | 0.77 | 20 | empty |
| 2 | 68 | 0.44 | 0.82 | 18 | MG, TPP |
| 3 | 92 | 0.40 | 0.78 | 20 | empty |
| 4 | 86 | 0.40 | 0.78 | 14 | empty |
| 5 | 79 | 0.37 | 0.76 | 17 | EDO |
Compared structures
- 4KXW · Human transketolase in covalent complex with donor ketose D-xylulose-5-phosphate, crystal… · the same entry in another collection · chain A against A, TM-score 1.00
- P29401 · AlphaFold monomer V2.0 prediction for transketolase (P29401) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P29401
- Elsewhere: RCSB PDB 4KXW · PDBe 4KXW · UniProt P29401
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