Research workbench
Crystal structure of RCAR3:PP2C wild-type with (+)-aba
Analyse Crystal structure of RCAR3:PP2C wild-type with (+)-aba in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GWP
- Type
- protein
- Length
- 920 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
- 12 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable protein phosphatase 2C 50 (EC 3.1.3.16) | protein | 305 | 35% helix, 30% strand | Q6L5H6 |
| B | Probable protein phosphatase 2C 50 (EC 3.1.3.16) | protein | 305 | 32% helix, 30% strand | Q6L5H6 |
| C | Aba receptor RCAR3 | protein | 161 | 22% helix, 40% strand | K4N2F7 |
| D | Aba receptor RCAR3 | protein | 149 | 24% helix, 41% 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 · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 244 | 0.86 | 0.97 | 40 | A8S |
| 2 | 230 | 0.84 | 0.96 | 40 | A8S |
| 3 | 697 | 0.71 | 0.78 | 59 | empty |
| 4 | 332 | 0.57 | 0.76 | 34 | MG |
| 5 | 299 | 0.53 | 0.75 | 32 | MG |
Interfaces
5 interfaces between chains.
- B–D · 924 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 915 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 328 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 290 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 20 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
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 5GWP · PDBe 5GWP · UniProt Q6L5H6 · UniProt K4N2F7
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