Research workbench
14-3-3 sigma in complex with hdmx-342+367 peptide
Analyse 14-3-3 sigma in complex with hdmx-342+367 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YR7
- Type
- protein
- Length
- 476 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 14-3-3 protein sigma; Protein MDM4
- UniProt
- P31947, O15151
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 14-3-3 protein sigma | protein | 230 | 80% helix, 0% strand | P31947 |
| Q, C | Protein MDM4 | protein | 8 | 38% helix, 0% strand | O15151 |
Ligands and binding sites
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 216 | 0.61 | 0.81 | 25 | empty |
| 2 | 324 | 0.58 | 0.77 | 46 | empty |
| 3 | 253 | 0.46 | 0.73 | 22 | empty |
| 4 | 61 | 0.40 | 0.80 | 19 | empty |
| 5 | 55 | 0.39 | 0.81 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1016 Ų buried · 14 hydrogen bonds · protein-protein
- B–Q · 561 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 547 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 6YR7 · 14-3-3 sigma in complex with hDMX-342+367 peptide · 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 A against A, TM-score 0.96
- O15151 · AlphaFold monomer V2.0 prediction for protein MDM4 (O15151) · a predicted model of the same protein · chain Q against A, TM-score 0.45
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
- Every structure of UniProt O15151
- Elsewhere: RCSB PDB 6YR7 · PDBe 6YR7 · UniProt P31947 · UniProt O15151
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