Research workbench
Crystal structure of 14-3-3ZETA in complex with a 8-carbon-linker cyclic peptide derived from exos
Analyse Crystal structure of 14-3-3ZETA in complex with a 8-carbon-linker cyclic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4N7Y
- Type
- protein
- Length
- 473 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 14-3-3 protein ZETA/DELTA; Exoenzyme S
- UniProt
- P63104, Q93SQ3
- Ligands
- 2JN
- Pockets
- 1 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 80% 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 | 223 | 81% helix, 0% strand | P63104 |
| C, D | Exoenzyme S | protein | 10 | 0% helix, 0% strand | Q93SQ3 |
Ligands and binding sites
- 2JN · 2-methyl-D-norleucine · ligand · 2 copies · chains A, C, B, D
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 | 343 | 0.55 | 0.75 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1037 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 762 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 711 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- 4N7Y · Crystal structure of 14-3-3zeta in complex with a 8-carbon-linker cyclic peptide derived… · 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 0.99
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 P63104
- Every structure of UniProt Q93SQ3
- Elsewhere: RCSB PDB 4N7Y · PDBe 4N7Y · UniProt P63104 · UniProt Q93SQ3
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