Research workbench
Crystal structure of the a. thaliana dhq-dehydroshikimate-sdh- shikimate-NADP(H)
Analyse Crystal structure of the a. thaliana dhq-dehydroshikimate-sdh- shikimate-NADP(H) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2O7Q
- Type
- protein
- Length
- 501 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional 3-dehydroquinate DEHYDRATASE/SHIKIMATE dehydrogenase
- EC
- 1.1.1.25, 4.2.1.10
- UniProt
- Q9SQT8
- Ligands
- DHK, SO4
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional 3-dehydroquinate DEHYDRATASE/SHIKIMATE dehydrogenase (EC 1.1.1.25, 4.2.1.10) | protein | 501 | 41% helix, 21% strand | Q9SQT8 |
Ligands and binding sites
- DHK · 3-dehydroshikimate · ligand · 2 copies · chains A
- SO4 · Sulfate ion · ion · 3 copies · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 295 | 0.76 | 0.88 | 50 | SO4, DHK |
| 2 | 65 | 0.61 | 0.91 | 19 | DHK |
| 3 | 176 | 0.49 | 0.76 | 29 | empty |
| 4 | 70 | 0.38 | 0.78 | 15 | empty |
Modifications
Observed in the structure: 2 modified, 1 covalent (oxidation, covalent ligand).
Compared structures
- 2O7Q · Crystal Structure of the A. thaliana DHQ-dehydroshikimate-SDH-shikimate-NADP(H) · 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 2O7Q · PDBe 2O7Q · UniProt Q9SQT8
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