MolNFT v1 · #102030 · protein
Crystal structure of qdta, a sugar 3,4-ketoisemerase from thermoanaerobacterium thermosaccharolyticum in complex with tdp
4O9E: “Crystal structure of qdta, a sugar 3,4-ketoisemerase from thermoanaerobacterium thermosaccharolyticum in…”. X-ray diffraction, 3 ligands (TYD, TDR, 4TD), 2 pockets (best druggability 0.47). MolNFT v1 #102030 on GenesisL1: 3D…
- PDB
- 4O9E
- Type
- protein
- Length
- 274 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Qdta
- UniProt
- Q6TFC5
- Ligands
- TYD, TDR, 4TD
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Qdta | protein | 137 | 11% helix, 49% strand | Q6TFC5 |
Ligands and binding sites
- TYD · Thymidine-5'-diphosphate · ligand · 2 copies · chains A, B
- TDR · Thymine · ligand · chains A
- 4TD · (2S)-1-[3-[(2S)-2-oxidanylpropoxy]-2-[[(2S)-2-oxidanylpropoxy]methyl]-2-[[(2R)-2-oxidanylpropoxy]methyl]propoxy]propan-2-ol · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 140 | 0.47 | 0.78 | 22 | TYD |
| 2 | 146 | 0.47 | 0.77 | 24 | TYD |
Interfaces
1 interface between chains.
- A–B · 1639 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 4O9E · Crystal structure of QdtA, a sugar 3,4-ketoisemerase from Thermoanaerobacterium… · 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 Q6TFC5
- Elsewhere: RCSB PDB 4O9E · PDBe 4O9E · UniProt Q6TFC5
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