MolNFT v1 · #141744 · protein
Crystal structure of OSD14 in complex with covalently bound KK094
5ZHR · Strigolactone esterase D14: “Crystal structure of OSD14 in complex with covalently bound KK094”. X-ray diffraction, 1 ligand (KOK), 4 pockets (best druggability 0.68). MolNFT v1 #141744 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5ZHR
- 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
- KOK
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Strigolactone esterase D14 (EC 3.1.-.-) | protein | 265 | 48% helix, 15% strand | Q10QA5 |
Ligands and binding sites
- KOK · (2,3-dihydro-1H-indol-1-yl)(1h-1,2,3-triazol-1-yl) methanone · 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 | 123 | 0.68 | 0.89 | 17 | KOK |
| 2 | 166 | 0.67 | 0.86 | 20 | KOK |
| 3 | 167 | 0.49 | 0.77 | 27 | empty |
| 4 | 148 | 0.48 | 0.78 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 599 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5ZHR · Crystal structure of OsD14 in complex with covalently bound KK094 · 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 B 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 5ZHR · PDBe 5ZHR · UniProt Q10QA5
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