MolNFT v1 · #141588 · protein
Crystal structure of OSPP2C50 S265L/I267V:OSPYL/RCAR3 with (+)-aba
5ZCG · Probable protein phosphatase 2C 50: “Crystal structure of OSPP2C50 S265L/I267V:OSPYL/RCAR3 with (+)-aba”. X-ray diffraction, 2 ligands (A8S, MG), 10 pockets (best druggability 0.85). MolNFT v1 #141588 on GenesisL1: 3D structure…
- PDB
- 5ZCG
- Type
- protein
- Length
- 941 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable protein phosphatase 2C 50; Aba receptor RCAR3
- EC
- 3.1.3.16
- UniProt
- Q6L5H6, K4N2F7
- Ligands
- A8S, MG
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable protein phosphatase 2C 50 (EC 3.1.3.16) | protein | 306 | 34% helix, 29% strand | Q6L5H6 |
| B | Probable protein phosphatase 2C 50 (EC 3.1.3.16) | protein | 308 | 33% helix, 30% strand | Q6L5H6 |
| C | Aba receptor RCAR3 | protein | 160 | 24% helix, 41% strand | K4N2F7 |
| D | Aba receptor RCAR3 | protein | 167 | 26% helix, 39% strand | K4N2F7 |
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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 242 | 0.85 | 0.97 | 40 | A8S |
| 2 | 218 | 0.84 | 0.96 | 29 | A8S |
| 3 | 342 | 0.59 | 0.77 | 35 | MG |
| 4 | 348 | 0.58 | 0.77 | 36 | empty |
| 5 | 87 | 0.37 | 0.75 | 14 | empty |
Interfaces
4 interfaces between chains.
- A–C · 931 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 875 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 288 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 274 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5ZCG · Crystal structure of OsPP2C50 S265L/I267V:OsPYL/RCAR3 with (+)-ABA · the same entry in another collection · chain A against A, 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
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 K4N2F7
- Elsewhere: RCSB PDB 5ZCG · PDBe 5ZCG · UniProt Q6L5H6 · UniProt K4N2F7
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