MolNFT v1 · #126443 · protein
The molecular tweezer CLR01 stabilizes a disordered protein-protein interface
5M35 · 14-3-3 protein ZETA/DELTA: “The molecular tweezer CLR01 stabilizes a disordered protein-protein interface”. X-ray diffraction, 1 ligand (BEZ), 5 pockets (best druggability 0.64). MolNFT v1 #126443 on GenesisL1: 3D structure, binding…
- PDB
- 5M35
- Type
- protein
- Length
- 468 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
- BEZ
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 14-3-3 protein ZETA/DELTA | protein | 228 | 80% helix, 0% strand | P63104 |
| B | 14-3-3 protein ZETA/DELTA | protein | 223 | 81% helix, 0% strand | P63104 |
| C | M-phase inducer phosphatase 3 (EC 3.1.3.48) | protein | 10 | 0% helix, 0% strand | P30307 |
| D | M-phase inducer phosphatase 3 (EC 3.1.3.48) | protein | 7 | 0% helix, 0% strand | P30307 |
Ligands and binding sites
- BEZ · Benzoic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 276 | 0.64 | 0.81 | 27 | empty |
| 2 | 173 | 0.57 | 0.81 | 27 | empty |
| 3 | 290 | 0.52 | 0.75 | 26 | empty |
| 4 | 93 | 0.34 | 0.74 | 16 | empty |
| 5 | 93 | 0.34 | 0.74 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–B · 949 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 577 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 460 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation, phosphorylation).
Compared structures
- 5M35 · 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 B 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 D against A, TM-score 0.42
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 5M35 · PDBe 5M35 · UniProt P63104 · UniProt P30307
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