MolNFT v1 · #144197 · protein
Crystal structure of arabidopsis dehydroquinate dehydratase-shikimate dehydrogenase (T381G mutant) in complex with tartrate and shikimate
6BMB · Bifunctional 3-dehydroquinate DEHYDRATASE/SHIKIMATE…: “Crystal structure of arabidopsis dehydroquinate dehydratase-shikimate dehydrogenase (T381G mutant) in complex…”. X-ray diffraction, 2 ligands (SKM, SO4), 5 pockets (best…
- PDB
- 6BMB
- Type
- protein
- Length
- 498 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional 3-dehydroquinate DEHYDRATASE/SHIKIMATE dehydrogenase, chloroplastic
- EC
- 4.2.1.10, 1.1.1.25
- UniProt
- Q9SQT8
- Ligands
- SKM, SO4
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional 3-dehydroquinate DEHYDRATASE/SHIKIMATE dehydrogenase, chloroplastic (EC 4.2.1.10, 1.1.1.25) | protein | 498 | 41% 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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.82 | 0.96 | 32 | SKM |
| 2 | 71 | 0.64 | 0.92 | 18 | TLA |
| 3 | 159 | 0.47 | 0.76 | 28 | empty |
| 4 | 85 | 0.43 | 0.79 | 17 | empty |
| 5 | 95 | 0.38 | 0.76 | 22 | SO4 |
Compared structures
- 6BMB · Crystal structure of Arabidopsis Dehydroquinate dehydratase-shikimate dehydrogenase… · 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 6BMB · PDBe 6BMB · UniProt Q9SQT8
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