MolNFT v1 · #38190 · protein
Crystal structure of arabidopsis dehydroquinate dehydratase- shikimate dehydrogenase in complex with tartrate and shikimate
2GPT · 3-dehydroquinate dehydratase/ shikimate 5- dehydrogenase: “Crystal structure of arabidopsis dehydroquinate dehydratase- shikimate dehydrogenase in complex with tartrate…”. X-ray diffraction, 2 ligands (SKM, SO4), 4 pockets (best…
- PDB
- 2GPT
- Type
- protein
- Length
- 498 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-dehydroquinate dehydratase/ shikimate 5- dehydrogenase
- EC
- 4.2.1.10, 1.1.1.25
- UniProt
- Q9SQT8
- Ligands
- SKM, SO4
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-dehydroquinate dehydratase/ shikimate 5- dehydrogenase (EC 4.2.1.10, 1.1.1.25) | protein | 498 | 40% helix, 20% strand | Q9SQT8 |
Ligands and binding sites
- SKM · (3R,4S,5R)-3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- TLA · L(+)-tartaric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.75 | 0.88 | 45 | SO4, SKM |
| 2 | 95 | 0.65 | 0.90 | 24 | TLA |
| 3 | 159 | 0.50 | 0.78 | 26 | empty |
| 4 | 59 | 0.38 | 0.79 | 13 | empty |
Compared structures
- 2GPT · Crystal structure of Arabidopsis Dehydroquinate dehydratase-shikimate dehydrogenase in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9SQT8 · AlphaFold monomer V2.0 prediction for bifunctional 3-dehydroquinate DEHYDRATASE/SHIKIMATE… · 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 Q9SQT8
- Elsewhere: RCSB PDB 2GPT · PDBe 2GPT · UniProt Q9SQT8
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