MolNFT v1 · #13793 · protein
Retro-diels-alderase catalytic antibody
1LO2 · If kappa light chain: “Retro-diels-alderase catalytic antibody”. X-ray diffraction, 1 ligand (OX1), 10 pockets (best druggability 0.64). MolNFT v1 #13793 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1LO2
- Type
- protein
- Length
- 878 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- If kappa light chain; Ig gamma 2A heavy chain
- UniProt
- Q99M37
- Ligands
- OX1
- Pockets
- 10 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X, L | If kappa light chain | protein | 219 | 6% helix, 50% strand | Q99M37 |
| Y, H | Ig gamma 2A heavy chain | protein | 220 | 4% helix, 51% strand | — |
Ligands and binding sites
- OX1 · [2'-carboxylethyl]-10-methyl-anthracene endoperoxide · ligand · 2 copies · chains X, Y, L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.64 | 0.86 | 21 | OX1 |
| 2 | 159 | 0.63 | 0.85 | 23 | OX1 |
| 3 | 454 | 0.58 | 0.74 | 59 | empty |
| 4 | 341 | 0.56 | 0.75 | 43 | empty |
| 5 | 256 | 0.51 | 0.74 | 28 | empty |
Interfaces
3 interfaces between chains.
- L–H · 2014 Ų buried · 22 hydrogen bonds · protein-protein
- X–Y · 1972 Ų buried · 19 hydrogen bonds · protein-protein
- Y–L · 433 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 1LO2 · Retro-Diels-Alderase Catalytic Antibody · the same entry in another collection · chain X against X, 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
- Every structure of UniProt Q99M37
- Elsewhere: RCSB PDB 1LO2 · PDBe 1LO2 · UniProt Q99M37
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