MolNFT v1 · #95133 · protein
Crystal structure of rice DWARF14 (D14) in complex with a GR24 hydrolysis intermediate
4IHA · Dwarf 88 esterase: “Crystal structure of rice DWARF14 (D14) in complex with a GR24 hydrolysis intermediate”. X-ray diffraction, 1 ligand (OPL), 5 pockets (best druggability 0.70). MolNFT v1 #95133 on GenesisL1: 3D structure, binding…
- PDB
- 4IHA
- Type
- protein
- Length
- 536 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dwarf 88 esterase
- UniProt
- Q10QA5
- Ligands
- OPL
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dwarf 88 esterase | protein | 268 | 46% helix, 16% strand | Q10QA5 |
Ligands and binding sites
- OPL · (2R,3R)-2,4,4-trihydroxy-3-methylbutanal · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 177 | 0.70 | 0.87 | 23 | OPL |
| 2 | 139 | 0.70 | 0.89 | 22 | OPL |
| 3 | 235 | 0.50 | 0.75 | 33 | empty |
| 4 | 66 | 0.38 | 0.79 | 15 | empty |
| 5 | 87 | 0.33 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 583 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4IHA · Crystal structure of rice DWARF14 (D14) in complex with a GR24 hydrolysis intermediate · 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 4IHA · PDBe 4IHA · UniProt Q10QA5
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