Research workbench
Crystal structure of 309M3-B in complex with trimethylated lys
Analyse Crystal structure of 309M3-B in complex with trimethylated lys in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YHY
- Type
- protein
- Length
- 856 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab light chain; Fab heavy chain
- Ligands
- M3L
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, L | Fab light chain | protein | 210 | 8% helix, 50% strand | — |
| B, H | Fab heavy chain | protein | 218 | 8% helix, 54% strand | — |
Ligands and binding sites
- M3L · N-trimethyllysine · ligand · 2 copies · chains C, B, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 606 | 0.63 | 0.75 | 58 | empty |
| 2 | 538 | 0.61 | 0.74 | 60 | empty |
| 3 | 55 | 0.55 | 0.90 | 21 | empty |
| 4 | 52 | 0.54 | 0.89 | 19 | empty |
| 5 | 65 | 0.29 | 0.73 | 15 | empty |
Interfaces
2 interfaces between chains.
- H–L · 1753 Ų buried · 19 hydrogen bonds · protein-protein
- C–B · 1747 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4YHY · Crystal structure of 309M3-B in complex with trimethylated Lys · the same entry in another collection · chain C against C, 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 4YHY · PDBe 4YHY
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