MolNFT v1 · #47840 · protein
Structure of a H51N mutant dtdp-4-keto-6-deoxy-D-glucose-3,4- ketoisomerase from aneurinibacillus thermoaerophilus complexed with tdp
2PAK · Dtdp-6-deoxy-3,4-keto-hexulose isomerase: “Structure of a H51N mutant dtdp-4-keto-6-deoxy-D-glucose-3,4- ketoisomerase from aneurinibacillus…”. X-ray diffraction, 1 ligand (TYD), 2 pockets (best druggability 0.54). MolNFT v1 #47840…
- PDB
- 2PAK
- Type
- protein
- Length
- 269 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dtdp-6-deoxy-3,4-keto-hexulose isomerase
- EC
- 5.3.1.-
- UniProt
- Q6T1W8
- Ligands
- TYD
- Pockets
- 2 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dtdp-6-deoxy-3,4-keto-hexulose isomerase (EC 5.3.1.-) | protein | 135 | 12% helix, 47% strand | Q6T1W8 |
| B | Dtdp-6-deoxy-3,4-keto-hexulose isomerase (EC 5.3.1.-) | protein | 134 | 10% helix, 47% strand | Q6T1W8 |
Ligands and binding sites
- TYD · Thymidine-5'-diphosphate · ligand · 2 copies · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 149 | 0.54 | 0.81 | 23 | TYD |
| 2 | 162 | 0.50 | 0.78 | 22 | TYD |
Interfaces
1 interface between chains.
- A–B · 1757 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 2PAK · Structure of a H51N mutant dTDP-4-keto-6-deoxy-D-glucose-3,4-ketoisomerase from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6T1W8 · AlphaFold monomer V2.0 prediction for tdp-4-oxo-6-deoxy-alpha-D- glucose-3,4-oxoisomerase… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q6T1W8
- Elsewhere: RCSB PDB 2PAK · PDBe 2PAK · UniProt Q6T1W8
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