MolNFT v1 · #29055 · protein
Crystal structure of the human sigma isoform of 14-3-3 in complex with a mode-1 phosphopeptide
1YWT · 14-3-3 protein sigma: “Crystal structure of the human sigma isoform of 14-3-3 in complex with a mode-1 phosphopeptide”. X-ray diffraction, 1 ligand (CA), 5 pockets (best druggability 0.59). MolNFT v1 #29055 on GenesisL1: 3D…
- PDB
- 1YWT
- Type
- protein
- Length
- 460 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 14-3-3 protein sigma; Sythetic optimal phosphopeptide (mode-1)
- UniProt
- P31947
- Ligands
- CA
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 14-3-3 protein sigma | protein | 223 | 83% helix, 0% strand | P31947 |
| B | 14-3-3 protein sigma | protein | 222 | 82% helix, 0% strand | P31947 |
| C | Sythetic optimal phosphopeptide (mode-1) | protein | 6 | 0% helix, 0% strand | — |
| D | Sythetic optimal phosphopeptide (mode-1) | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · chains 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 | 410 | 0.59 | 0.75 | 30 | empty |
| 2 | 110 | 0.58 | 0.85 | 22 | empty |
| 3 | 77 | 0.52 | 0.85 | 20 | empty |
| 4 | 144 | 0.41 | 0.75 | 21 | empty |
| 5 | 71 | 0.30 | 0.74 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1014 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 685 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 526 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 1YWT · Crystal structure of the human sigma isoform of 14-3-3 in complex with a mode-1… · the same entry in another collection · chain A against A, TM-score 1.00
- P31947 · AlphaFold monomer V2.0 prediction for 14-3-3 protein sigma (P31947) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P31947
- Elsewhere: RCSB PDB 1YWT · PDBe 1YWT · UniProt P31947
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