MolNFT v1 · #13791 · protein
Catalytic retro-diels-alderase transition state analogue complex
1LO0 · If kappa light chain: “Catalytic retro-diels-alderase transition state analogue complex”. X-ray diffraction, 1 ligand (BC1), 11 pockets (best druggability 0.63). MolNFT v1 #13791 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1LO0
- 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
- P01837, P01865
- Ligands
- BC1
- Pockets
- 11 · best druggability 0.63
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 | 5% helix, 50% strand | P01837 |
| Y, H | Ig gamma 2A heavy chain | protein | 220 | 4% helix, 51% strand | P01865 |
Ligands and binding sites
- BC1 · 3-{[(9-cyano-9,10-dihydro-10-methylacridin-9-yl)carbonyl]amino}propanoic acid · ligand · 2 copies · chains X, Y, L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.63 | 0.87 | 22 | BC1 |
| 2 | 131 | 0.60 | 0.85 | 23 | BC1 |
| 3 | 434 | 0.59 | 0.75 | 59 | empty |
| 4 | 429 | 0.57 | 0.74 | 60 | empty |
| 5 | 270 | 0.53 | 0.75 | 25 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1992 Ų buried · 21 hydrogen bonds · protein-protein
- X–Y · 1970 Ų buried · 19 hydrogen bonds · protein-protein
- Y–L · 431 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 1LO0 · Catalytic Retro-Diels-Alderase Transition State Analogue Complex · the same entry in another collection · chain X against X, TM-score 1.00
- P01865 · AlphaFold monomer V2.0 prediction for ig gamma-2A chain C region, membrane-bound form… · a predicted model of the same protein · chain Y against A, TM-score 0.49
- P01837 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa constant (P01837) · a predicted model of the same protein · chain X 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 P01837
- Every structure of UniProt P01865
- Elsewhere: RCSB PDB 1LO0 · PDBe 1LO0 · UniProt P01837 · UniProt P01865
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.