MolNFT v1 · #123500 · protein
Crystal structure of 14-3-3ZETA in complex with a cyclic peptide involving an adamantyl and a dicarboxy side chain
5JM4 · 14-3-3 protein ZETA/DELTA: “Crystal structure of 14-3-3ZETA in complex with a cyclic peptide involving an adamantyl and a dicarboxy side…”. X-ray diffraction, 1 ligand (BEZ), 1 pocket (best druggability 0.51). MolNFT v1 #123500 on…
- PDB
- 5JM4
- Type
- protein
- Length
- 479 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 14-3-3 protein ZETA/DELTA; Gln-gly-mkd-ang-asp-mkd-leu-asp-leu-ala-clu
- UniProt
- P63104
- Ligands
- BEZ
- Pockets
- 1 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 83% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 14-3-3 protein ZETA/DELTA | protein | 228 | 84% helix, 0% strand | P63104 |
| B | 14-3-3 protein ZETA/DELTA | protein | 229 | 84% helix, 0% strand | P63104 |
| D, E | Gln-gly-mkd-ang-asp-mkd-leu-asp-leu-ala-clu | protein | 11 | 36% helix, 0% strand | — |
Ligands and binding sites
- 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
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 266 | 0.51 | 0.75 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 912 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 792 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 768 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (nonstandard).
Compared structures
- 5JM4 · Crystal structure of 14-3-3zeta in complex with a cyclic peptide involving an adamantyl… · the same entry in another collection · chain A against A, 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 0.97
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
- Elsewhere: RCSB PDB 5JM4 · PDBe 5JM4 · UniProt P63104
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