Research workbench
Crystal structure of 14-3-3 zeta in complex with a serine 124- phosphorylated TBC1D7 peptide
Analyse Crystal structure of 14-3-3 zeta in complex with a serine 124- phosphorylated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ULO
- Type
- protein
- Length
- 462 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 14-3-3 protein ZETA/DELTA; TBC1 domain family member 7
- UniProt
- P63104, Q5SZL8
- Ligands
- LPD, UNX
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 4 distinct chains · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 14-3-3 protein ZETA/DELTA | protein | 225 | 83% helix, 0% strand | P63104 |
| B | 14-3-3 protein ZETA/DELTA | protein | 228 | 83% helix, 0% strand | P63104 |
| C | TBC1 domain family member 7 | protein | 4 | 0% helix, 0% strand | Q5SZL8 |
| D | TBC1 domain family member 7 | protein | 5 | 0% helix, 0% strand | Q5SZL8 |
Ligands and binding sites
- LPD · L-prolinamide · ligand · 2 copies · chains A, C, B, D
- UNX · Unknown atom or ion · ion · 8 copies · chains A, B, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
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 | 220 | 0.58 | 0.80 | 27 | LPD |
| 2 | 201 | 0.58 | 0.80 | 23 | LPD |
| 3 | 325 | 0.54 | 0.75 | 25 | EDO, UNX |
| 4 | 51 | 0.26 | 0.74 | 14 | UNX |
Interfaces
3 interfaces between chains.
- A–B · 999 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 443 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 412 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, phosphorylation).
Compared structures
- 5ULO · Crystal Structure of 14-3-3 zeta in Complex with a Serine 124-phosphorylated TBC1D7… · 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 Q5SZL8
- Elsewhere: RCSB PDB 5ULO · PDBe 5ULO · UniProt P63104 · UniProt Q5SZL8
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