Research workbench
The molecular tweezer CLR01 stabilizes a disordered protein-protein interface
Analyse The molecular tweezer CLR01 stabilizes a disordered protein-protein interface in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M37
- Type
- protein
- Length
- 491 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 14-3-3 protein ZETA/DELTA; M-phase inducer phosphatase 3
- EC
- 3.1.3.48
- UniProt
- P63104, P30307
- Ligands
- 9SZ, BEZ
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 14-3-3 protein ZETA/DELTA | protein | 230 | 82% helix, 0% strand | P63104 |
| B | 14-3-3 protein ZETA/DELTA | protein | 227 | 82% helix, 0% strand | P63104 |
| C | M-phase inducer phosphatase 3 (EC 3.1.3.48) | protein | 17 | 0% helix, 0% strand | P30307 |
| D | M-phase inducer phosphatase 3 (EC 3.1.3.48) | protein | 17 | 0% helix, 0% strand | P30307 |
Ligands and binding sites
- 9SZ · C42 H32 O8 P2 · ligand · 4 copies · chains A, B, C, D
- BEZ · Benzoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 343 | 0.70 | 0.83 | 40 | empty |
| 2 | 312 | 0.67 | 0.82 | 38 | empty |
| 3 | 446 | 0.58 | 0.75 | 41 | empty |
| 4 | 149 | 0.52 | 0.80 | 17 | 9SZ |
| 5 | 133 | 0.46 | 0.78 | 18 | 9SZ |
Interfaces
3 interfaces between chains.
- A–B · 946 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 802 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 740 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 5M37 · The molecular tweezer CLR01 stabilizes a disordered protein-protein interface · the same entry in another collection · chain D against D, TM-score 1.00
- P63104 · AlphaFold monomer V2.0 prediction for 14-3-3 protein ZETA/DELTA (P63104) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P30307 · AlphaFold monomer V2.0 prediction for M-phase inducer phosphatase 3 (P30307) · a predicted model of the same protein · chain C against A, TM-score 0.23
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 P63104
- Every structure of UniProt P30307
- Elsewhere: RCSB PDB 5M37 · PDBe 5M37 · UniProt P63104 · UniProt P30307
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