Research workbench
Crystal structure of OSD14 in complex with D-ring-opened 7'-carba-4BD
Analyse Crystal structure of OSD14 in complex with D-ring-opened 7'-carba-4BD in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YZ7
- Type
- protein
- Length
- 530 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Strigolactone esterase D14
- EC
- 3.1.-.-
- UniProt
- Q10QA5
- Ligands
- 94X
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Strigolactone esterase D14 (EC 3.1.-.-) | protein | 265 | 47% helix, 15% strand | Q10QA5 |
Ligands and binding sites
- 94X · (2Z,4S)-5-(4-bromophenyl)-4-hydroxy-2-methylpent-2-enoic acid · ligand · 2 copies · chains A, B
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 | 166 | 0.70 | 0.88 | 21 | 94X |
| 2 | 150 | 0.68 | 0.88 | 20 | 94X |
| 3 | 109 | 0.38 | 0.75 | 24 | empty |
| 4 | 88 | 0.33 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 623 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5YZ7 · Crystal structure of OsD14 in complex with D-ring-opened 7'-carba-4BD · the same entry in another collection · chain A against A, TM-score 1.00
- Q10QA5 · AlphaFold monomer V2.0 prediction for strigolactone esterase D14 (Q10QA5) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 Q10QA5
- Elsewhere: RCSB PDB 5YZ7 · PDBe 5YZ7 · UniProt Q10QA5
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