Research workbench
Crystal structure of ZMYND8 phd-bromo-pwwp tandem in complex with drebrin adf-H domain
Analyse Crystal structure of ZMYND8 phd-bromo-pwwp tandem in complex with drebrin adf-H… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y1Z
- Type
- protein
- Length
- 874 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Drebrin; Protein kinase C-binding protein 1
- UniProt
- Q16643, Q9ULU4
- Ligands
- ZN, SO4
- Pockets
- 14 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Drebrin | protein | 130 | 35% helix, 28% strand | Q16643 |
| B | Drebrin | protein | 135 | 33% helix, 28% strand | Q16643 |
| C | Protein kinase C-binding protein 1 | protein | 302 | 44% helix, 12% strand | Q9ULU4 |
| D | Protein kinase C-binding protein 1 | protein | 307 | 45% helix, 12% strand | Q9ULU4 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains C, D
- SO4 · Sulfate ion · ion · 6 copies · chains A, C, D
- GOL · Glycerol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 305 | 0.73 | 0.86 | 39 | empty |
| 2 | 596 | 0.72 | 0.80 | 73 | empty |
| 3 | 168 | 0.51 | 0.78 | 33 | empty |
| 4 | 173 | 0.51 | 0.78 | 36 | empty |
| 5 | 78 | 0.49 | 0.83 | 19 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1123 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 987 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 302 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5Y1Z · Crystal structure of ZMYND8 PHD-BROMO-PWWP tandem in complex with Drebrin ADF-H domain · the same entry in another collection · chain D against D, TM-score 1.00
- Q16643 · AlphaFold monomer V2.0 prediction for drebrin (Q16643) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9ULU4 · AlphaFold monomer V2.0 prediction for protein kinase C-binding protein 1 (Q9ULU4) · a predicted model of the same protein · chain C 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 Q16643
- Every structure of UniProt Q9ULU4
- Elsewhere: RCSB PDB 5Y1Z · PDBe 5Y1Z · UniProt Q16643 · UniProt Q9ULU4
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