Research workbench
X-ray structure if the qdta 3,4-ketoisomerase from thermoanaerobacterium thermosaccharolyticum, double mutant Y17R/R97H, in complex with tdp
Analyse X-ray structure if the qdta 3,4-ketoisomerase from thermoanaerobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZU7
- Type
- protein
- Length
- 1,097 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Qdta
- UniProt
- Q6TFC5
- Ligands
- TYD, PXN
- Pockets
- 18 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Qdta | protein | 137 | 11% helix, 49% strand | Q6TFC5 |
| B, C, F | Qdta | protein | 138 | 11% helix, 50% strand | Q6TFC5 |
| E | Qdta | protein | 137 | 11% helix, 48% strand | Q6TFC5 |
| G, H | Qdta | protein | 136 | 10% helix, 49% strand | Q6TFC5 |
Ligands and binding sites
- TYD · Thymidine-5'-diphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- PXN · (2S)-1-[3-{[(2R)-2-hydroxypropyl]oxy}-2,2-bis({[(2R)-2-hydroxypropyl]oxy}methyl)propoxy]propan-2-ol · ligand · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 253 | 0.60 | 0.80 | 41 | TYD |
| 2 | 263 | 0.59 | 0.79 | 37 | TYD |
| 3 | 241 | 0.57 | 0.78 | 35 | TYD |
| 4 | 208 | 0.56 | 0.79 | 20 | empty |
| 5 | 234 | 0.55 | 0.78 | 28 | TYD |
Interfaces
8 interfaces between chains.
- E–F · 1736 Ų buried · 28 hydrogen bonds · protein-protein
- G–H · 1702 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1693 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1673 Ų buried · 28 hydrogen bonds · protein-protein
- D–F · 1190 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4ZU7 · X-ray structure if the QdtA 3,4-ketoisomerase from Thermoanaerobacterium… · the same entry in another collection · chain B against B, 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 4ZU7 · PDBe 4ZU7 · UniProt Q6TFC5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.