MolNFT v1 · #143096 · protein
Crystal structure of rice D14 bound to 2-(2-methyl-3-nitroanilino) benzoic acid
6AP8 · Strigolactone esterase D14: “Crystal structure of rice D14 bound to 2-(2-methyl-3-nitroanilino) benzoic acid”. X-ray diffraction, 1 ligand (BNY), 5 pockets (best druggability 0.71). MolNFT v1 #143096 on GenesisL1: 3D structure…
- PDB
- 6AP8
- Type
- protein
- Length
- 533 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
- BNY
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Strigolactone esterase D14 (EC 3.1.-.-) | protein | 266 | 48% helix, 15% strand | Q10QA5 |
| B | Strigolactone esterase D14 (EC 3.1.-.-) | protein | 267 | 49% helix, 16% strand | Q10QA5 |
Ligands and binding sites
- BNY · 2-[(2-methyl-3-nitrophenyl)amino]benzoic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 182 | 0.71 | 0.88 | 30 | BNY |
| 2 | 155 | 0.70 | 0.89 | 25 | BNY |
| 3 | 187 | 0.47 | 0.76 | 29 | empty |
| 4 | 171 | 0.47 | 0.76 | 32 | empty |
| 5 | 87 | 0.34 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 604 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6AP8 · Crystal Structure of rice D14 bound to 2-(2-methyl-3-nitroanilino)benzoic acid · 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 6AP8 · PDBe 6AP8 · UniProt Q10QA5
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