Research workbench
Crystal structure of the humanized apo LT3015 anti-lysophosphatidic acid antibody Fab fragment
Analyse Crystal structure of the humanized apo LT3015 anti-lysophosphatidic acid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QCT
- Type
- protein
- Length
- 437 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LT3015 antibody Fab fragment, heavy chain; LT3015 antibody Fab fragment, light chain
- UniProt
- Q6N089, P01834
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | LT3015 antibody Fab fragment, heavy chain | protein | 219 | 8% helix, 53% strand | Q6N089 |
| L | LT3015 antibody Fab fragment, light chain | protein | 218 | 5% helix, 50% strand | P01834 |
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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 233 | 0.48 | 0.74 | 34 | empty |
| 2 | 175 | 0.44 | 0.74 | 26 | empty |
| 3 | 99 | 0.39 | 0.76 | 25 | empty |
| 4 | 73 | 0.31 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- H–L · 1909 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3QCT · Crystal structure of the humanized apo LT3015 anti-lysophosphatidic acid antibody Fab… · the same entry in another collection · chain H against H, TM-score 1.00
- P01834 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa constant (P01834) · a predicted model of the same protein · chain L against A, TM-score 0.48
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 Q6N089
- Every structure of UniProt P01834
- Elsewhere: RCSB PDB 3QCT · PDBe 3QCT · UniProt Q6N089 · UniProt P01834
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.