Research workbench
Crystal structure of 304M3-B Fab in complex with H3K4ME3 peptide
Analyse Crystal structure of 304M3-B Fab in complex with H3K4ME3 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YHZ
- Type
- protein
- Length
- 439 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab heavy chain; Fab light chain; H3K4ME3 peptide
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fab heavy chain | protein | 219 | 10% helix, 53% strand | — |
| L | Fab light chain | protein | 211 | 7% helix, 50% strand | — |
| P | H3K4ME3 peptide | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 766 | 0.68 | 0.75 | 57 | empty |
| 2 | 235 | 0.50 | 0.75 | 25 | empty |
| 3 | 80 | 0.32 | 0.74 | 15 | empty |
| 4 | 56 | 0.32 | 0.76 | 13 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1819 Ų buried · 23 hydrogen bonds · protein-protein
- H–P · 232 Ų buried · 0 hydrogen bonds · protein-protein
- L–P · 165 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, methylation).
Compared structures
- 4YHZ · Crystal structure of 304M3-B Fab in complex with H3K4me3 peptide · the same entry in another collection · chain H against H, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 4YHZ · PDBe 4YHZ
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