Research workbench
Crystal structure of PYL13-PP2CA complex
Analyse Crystal structure of PYL13-PP2CA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4N0G
- Type
- protein
- Length
- 821 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein phosphatase 2C 37; Abscisic acid receptor PYL13
- EC
- 3.1.3.16
- UniProt
- P49598, Q9SN51
- Ligands
- MG, ZN
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein phosphatase 2C 37 (EC 3.1.3.16) | protein | 267 | 30% helix, 31% strand | P49598 |
| B | Protein phosphatase 2C 37 (EC 3.1.3.16) | protein | 265 | 31% helix, 32% strand | P49598 |
| C | Abscisic acid receptor PYL13 | protein | 145 | 26% helix, 41% strand | Q9SN51 |
| D | Abscisic acid receptor PYL13 | protein | 144 | 26% helix, 42% strand | Q9SN51 |
Ligands and binding sites
- MG · Magnesium ion · metal · 10 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 2 copies · chains A, B
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 | 222 | 0.84 | 0.97 | 31 | empty |
| 2 | 220 | 0.84 | 0.97 | 29 | empty |
| 3 | 242 | 0.56 | 0.78 | 33 | MG |
| 4 | 255 | 0.55 | 0.77 | 35 | MG |
| 5 | 82 | 0.36 | 0.76 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1103 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1055 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4N0G · Crystal Structure of PYL13-PP2CA complex · the same entry in another collection · chain D against D, TM-score 1.00
- P49598 · AlphaFold monomer V2.0 prediction for protein phosphatase 2C 37 (P49598) · a predicted model of the same protein · chain B against A, TM-score 1.00
- Q9SN51 · AlphaFold monomer V2.0 prediction for abscisic acid receptor PYL13 (Q9SN51) · a predicted model of the same protein · chain D 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 P49598
- Every structure of UniProt Q9SN51
- Elsewhere: RCSB PDB 4N0G · PDBe 4N0G · UniProt P49598 · UniProt Q9SN51
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