Research workbench
Crystal structure of RCAR3:PP2C wild-type with pyrabactin
Analyse Crystal structure of RCAR3:PP2C wild-type with pyrabactin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZCU
- Type
- protein
- Length
- 921 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
- PYV, MG, SO4
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable protein phosphatase 2C 50 (EC 3.1.3.16) | protein | 299 | 33% helix, 30% strand | Q6L5H6 |
| B | Probable protein phosphatase 2C 50 (EC 3.1.3.16) | protein | 298 | 34% helix, 31% strand | Q6L5H6 |
| C, D | Aba receptor RCAR3 | protein | 162 | 22% helix, 40% strand | K4N2F7 |
Ligands and binding sites
- PYV · 4-bromo-N-(pyridin-2-ylmethyl)naphthalene-1-sulfonamide · ligand · 2 copies · chains C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, C, 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 | 252 | 0.85 | 0.97 | 37 | PYV |
| 2 | 245 | 0.85 | 0.97 | 36 | PYV |
| 3 | 343 | 0.57 | 0.76 | 33 | MG, SO4 |
| 4 | 266 | 0.55 | 0.77 | 36 | MG, SO4 |
| 5 | 105 | 0.38 | 0.75 | 17 | empty |
Interfaces
4 interfaces between chains.
- A–C · 953 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 943 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 92 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 54 Ų buried · 1 hydrogen bond · protein-protein
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 5ZCU · PDBe 5ZCU · UniProt Q6L5H6 · UniProt K4N2F7
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