MolNFT v1 · #72910 · protein
Crystal structure of the abscisic receptor PYL2 in complex with pyrabactin
3NMH · Abscisic acid receptor PYL2: “Crystal structure of the abscisic receptor PYL2 in complex with pyrabactin”. X-ray diffraction, 1 ligand (PYV), 5 pockets (best druggability 0.87). MolNFT v1 #72910 on GenesisL1: 3D structure, binding…
- PDB
- 3NMH
- Type
- protein
- Length
- 529 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Abscisic acid receptor PYL2
- UniProt
- O80992
- Ligands
- PYV
- Pockets
- 5 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Abscisic acid receptor PYL2 | protein | 176 | 28% helix, 37% strand | O80992 |
| C | Abscisic acid receptor PYL2 | protein | 177 | 28% helix, 37% strand | O80992 |
Ligands and binding sites
- PYV · 4-bromo-N-(pyridin-2-ylmethyl)naphthalene-1-sulfonamide · ligand · 3 copies · chains A, B, C
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · 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 | 934 | 0.87 | 0.89 | 64 | PYV, EPE |
| 2 | 350 | 0.75 | 0.86 | 33 | PYV |
| 3 | 174 | 0.43 | 0.74 | 33 | empty |
| 4 | 156 | 0.42 | 0.74 | 23 | empty |
| 5 | 94 | 0.38 | 0.76 | 21 | empty |
Interfaces
2 interfaces between chains.
- A–B · 939 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 519 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3NMH · Crystal structure of the abscisic receptor PYL2 in complex with pyrabactin · the same entry in another collection · chain A against A, TM-score 1.00
- O80992 · AlphaFold monomer V2.0 prediction for abscisic acid receptor PYL2 (O80992) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 O80992
- Elsewhere: RCSB PDB 3NMH · PDBe 3NMH · UniProt O80992
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