MolNFT v1 · #102032 · protein
Crystal structure of the H51N mutant of the 3,4-ketoisomerase qdta from thermoanaerobacterium thermosaccharolyticum in complex with tdp- 4-keto-6-deoxyglucose
4O9G: “Crystal structure of the H51N mutant of the 3,4-ketoisomerase qdta from thermoanaerobacterium…”. X-ray diffraction, 2 ligands (T46, 4TD), 2 pockets (best druggability 0.57). MolNFT v1 #102032 on GenesisL1: 3D structure, binding…
- PDB
- 4O9G
- Type
- protein
- Length
- 276 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Qdta
- UniProt
- Q6TFC5
- Ligands
- T46, 4TD
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Qdta | protein | 138 | 11% helix, 49% strand | Q6TFC5 |
Ligands and binding sites
- T46 · dTDP-4-keto-6-deoxyglucose · ligand · 2 copies · chains A, B
- 4TD · (2S)-1-[3-[(2S)-2-oxidanylpropoxy]-2-[[(2S)-2-oxidanylpropoxy]methyl]-2-[[(2R)-2-oxidanylpropoxy]methyl]propoxy]propan-2-ol · ligand · chains B
- EDO · 1,2-ethanediol · additive · chains A, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.57 | 0.79 | 27 | T46 |
| 2 | 175 | 0.56 | 0.80 | 27 | T46, EDO |
Interfaces
1 interface between chains.
- A–B · 1630 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 4O9G · Crystal structure of the H51N mutant of the 3,4-ketoisomerase QdtA from… · 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 4O9G · PDBe 4O9G · UniProt Q6TFC5
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