Research workbench
Antibody structural organization: role of kappa - lambda chain constant domain switch in catalytic functionality
Analyse Antibody structural organization: role of kappa - lambda chain constant domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZL4
- Type
- protein
- Length
- 445 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- A17 antibody Fab fragment heavy chain; A17 antibody Fab fragment lambda light chain
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | A17 antibody Fab fragment heavy chain | protein | 231 | 7% helix, 48% strand | — |
| L | A17 antibody Fab fragment lambda light chain | protein | 214 | 6% helix, 49% strand | — |
Ligands and binding sites
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.78 | 0.98 | 19 | MES |
| 2 | 179 | 0.56 | 0.80 | 31 | empty |
| 3 | 401 | 0.53 | 0.73 | 45 | empty |
| 4 | 112 | 0.43 | 0.77 | 23 | empty |
| 5 | 85 | 0.32 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- H–L · 1921 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 3ZL4 · Antibody structural organization: Role of kappa - lambda chain constant domain switch in… · 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 3ZL4 · PDBe 3ZL4
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