MolNFT v1 · #114257 · protein
Crystal structure of human ZMYND8 phd-bromo-pwwp domain
5B73 · Protein kinase C-binding protein 1: “Crystal structure of human ZMYND8 phd-bromo-pwwp domain”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.56). MolNFT v1 #114257 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5B73
- Type
- protein
- Length
- 313 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein kinase C-binding protein 1
- UniProt
- Q9ULU4
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein kinase C-binding protein 1 | protein | 313 | 43% helix, 11% strand | Q9ULU4 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · 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 | 243 | 0.56 | 0.78 | 37 | empty |
| 2 | 183 | 0.53 | 0.78 | 32 | empty |
| 3 | 85 | 0.42 | 0.79 | 13 | empty |
| 4 | 56 | 0.42 | 0.82 | 17 | empty |
| 5 | 63 | 0.28 | 0.73 | 18 | empty |
Compared structures
- 5B73 · Crystal structure of human ZMYND8 PHD-Bromo-PWWP domain · the same entry in another collection · chain A against A, TM-score 1.00
- Q9ULU4 · AlphaFold monomer V2.0 prediction for protein kinase C-binding protein 1 (Q9ULU4) · a predicted model of the same protein · chain A 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 Q9ULU4
- Elsewhere: RCSB PDB 5B73 · PDBe 5B73 · UniProt Q9ULU4
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