MolNFT v1 · #172181 · protein
X-ray crystal structure of the CSPYL1-LIG1-HAB1 ternary complex
6ZUC: “X-ray crystal structure of the CSPYL1-LIG1-HAB1 ternary complex”. X-ray diffraction, 3 ligands (QPZ, MN, CL), 4 pockets (best druggability 0.84). MolNFT v1 #172181 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ZUC
- Type
- protein
- Length
- 489 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CSPYL1; Protein phosphatase 2C 16
- EC
- 3.1.3.16
- UniProt
- A0A067E666, Q9CAJ0
- Ligands
- QPZ, MN, CL
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CSPYL1 | protein | 187 | 28% helix, 36% strand | A0A067E666 |
| B | Protein phosphatase 2C 16 (EC 3.1.3.16) | protein | 302 | 33% helix, 30% strand | Q9CAJ0 |
Ligands and binding sites
- QPZ · 1,4-dimethyl-2-oxidanylidene-~{N}-(phenylmethyl) quinoline-6-sulfonamide · ligand · chains A
- MN · Manganese (II) ion · metal · 4 copies · chains B
- CL · Chloride ion · ion · 6 copies · chains B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 240 | 0.84 | 0.96 | 32 | QPZ |
| 2 | 67 | 0.73 | 0.98 | 19 | empty |
| 3 | 335 | 0.61 | 0.78 | 49 | MN, CL |
| 4 | 89 | 0.45 | 0.80 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 847 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6ZUC · X-RAY CRYSTAL STRUCTURE OF THE CsPYL1-Lig1-HAB1 TERNARY COMPLEX · the same entry in another collection · chain A against A, TM-score 1.00
- Q9CAJ0 · AlphaFold monomer V2.0 prediction for protein phosphatase 2C 16 (Q9CAJ0) · a predicted model of the same protein · chain B 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 A0A067E666
- Every structure of UniProt Q9CAJ0
- Elsewhere: RCSB PDB 6ZUC · PDBe 6ZUC · UniProt A0A067E666 · UniProt Q9CAJ0
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