Research workbench
Crystal structure of OSPP2C50 I267W:OSPYL/RCAR3 with (+)-aba
Analyse Crystal structure of OSPP2C50 I267W:OSPYL/RCAR3 with (+)-aba in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZCH
- Type
- protein
- Length
- 920 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein phosphatase 2C 50; Abscisic acid receptor PYL3
- EC
- 3.1.3.16
- UniProt
- Q6L5H6, Q6EN42
- Ligands
- A8S, MG
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein phosphatase 2C 50 (EC 3.1.3.16) | protein | 301 | 32% helix, 29% strand | Q6L5H6 |
| C | Abscisic acid receptor PYL3 | protein | 157 | 24% helix, 41% strand | Q6EN42 |
| B | Protein phosphatase 2C 50 (EC 3.1.3.16) | protein | 299 | 32% helix, 30% strand | Q6L5H6 |
| D | Abscisic acid receptor PYL3 | protein | 163 | 23% helix, 39% strand | Q6EN42 |
Ligands and binding sites
- A8S · (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid · ligand · 2 copies · chains C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 240 | 0.85 | 0.97 | 37 | A8S |
| 2 | 249 | 0.85 | 0.96 | 37 | A8S |
| 3 | 326 | 0.58 | 0.77 | 33 | MG |
| 4 | 300 | 0.55 | 0.76 | 34 | MG |
| 5 | 77 | 0.32 | 0.74 | 16 | empty |
Interfaces
4 interfaces between chains.
- B–D · 976 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 963 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 294 Ų buried · 7 hydrogen bonds · protein-protein
- C–B · 279 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5ZCH · Crystal structure of OsPP2C50 I267W:OsPYL/RCAR3 with (+)-ABA · the same entry in another collection · chain D against D, TM-score 1.00
- Q6L5H6 · AlphaFold monomer V2.0 prediction for protein phosphatase 2C 50 (Q6L5H6) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q6EN42 · AlphaFold monomer V2.0 prediction for abscisic acid receptor PYL3 (Q6EN42) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q6L5H6
- Every structure of UniProt Q6EN42
- Elsewhere: RCSB PDB 5ZCH · PDBe 5ZCH · UniProt Q6L5H6 · UniProt Q6EN42
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