MolNFT v1 · #121571 · protein
The crystal structure of the strigolactone-induced ATD14-D3-ASK1 complex
5HZG · Strigolactone esterase D14: “The crystal structure of the strigolactone-induced ATD14-D3-ASK1 complex”. X-ray diffraction, 1 ligand (6OM), 20 pockets (best druggability 0.77). MolNFT v1 #121571 on GenesisL1: 3D structure, binding…
- PDB
- 5HZG
- Type
- protein
- Length
- 2,005 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Strigolactone esterase D14; F-BOX/LRR-repeat MAX2 homolog; SKP1-like protein 1A
- EC
- 3.1.-.-
- UniProt
- Q9SQR3, Q5VMP0, Q39255
- Ligands
- 6OM
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 33% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Strigolactone esterase D14 (EC 3.1.-.-) | protein | 257 | 39% helix, 14% strand | Q9SQR3 |
| B | F-BOX/LRR-repeat MAX2 homolog | protein | 615 | 27% helix, 18% strand | Q5VMP0 |
| C | SKP1-like protein 1A | protein | 130 | 51% helix, 0% strand | Q39255 |
| F | F-BOX/LRR-repeat MAX2 homolog | protein | 614 | 28% helix, 17% strand | Q5VMP0 |
| G | SKP1-like protein 1A | protein | 132 | 51% helix, 0% strand | Q39255 |
Ligands and binding sites
- 6OM · (2Z)-2-methylbut-2-ene-1,4-diol · ligand · 2 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 212 | 0.77 | 0.92 | 44 | empty |
| 2 | 171 | 0.71 | 0.89 | 40 | empty |
| 3 | 169 | 0.69 | 0.88 | 31 | empty |
| 4 | 91 | 0.68 | 0.92 | 19 | empty |
| 5 | 178 | 0.66 | 0.86 | 27 | empty |
Interfaces
6 interfaces between chains.
- F–G · 2118 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 2054 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1590 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 1568 Ų buried · 22 hydrogen bonds · protein-protein
- B–E · 504 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5HZG · The crystal structure of the strigolactone-induced AtD14-D3-ASK1 complex · the same entry in another collection · chain G against G, TM-score 1.00
- Q5VMP0 · AlphaFold monomer V2.0 prediction for F-BOX/LRR-repeat MAX2 homolog (Q5VMP0) · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q9SQR3 · AlphaFold monomer V2.0 prediction for strigolactone esterase D14 (Q9SQR3) · a predicted model of the same protein · chain A against A, TM-score 0.90
- Q39255 · AlphaFold monomer V2.0 prediction for SKP1-like protein 1A (Q39255) · a predicted model of the same protein · chain G against A, TM-score 0.88
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 Q9SQR3
- Every structure of UniProt Q5VMP0
- Every structure of UniProt Q39255
- Elsewhere: RCSB PDB 5HZG · PDBe 5HZG · UniProt Q9SQR3 · UniProt Q5VMP0 · UniProt Q39255
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