Research workbench
Structure of a monoclonal antibody complexed with its MHC-I antigen
Analyse Structure of a monoclonal antibody complexed with its MHC-I antigen in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UYR
- Type
- protein
- Length
- 441 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody Fab heavy chain; Antibody Fab light chain; H-2 class I histocompatibility…
- UniProt
- P01897
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Antibody Fab heavy chain | protein | 215 | 8% helix, 55% strand | — |
| L | Antibody Fab light chain | protein | 218 | 6% helix, 52% strand | — |
| P | H-2 class I histocompatibility antigen, L-D alpha chain | protein | 8 | 38% helix, 0% strand | P01897 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · chains H, L, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 644 | 0.64 | 0.75 | 66 | empty |
| 2 | 124 | 0.41 | 0.75 | 21 | empty |
| 3 | 79 | 0.34 | 0.75 | 22 | empty |
| 4 | 74 | 0.31 | 0.74 | 20 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1762 Ų buried · 18 hydrogen bonds · protein-protein
- H–P · 354 Ų buried · 4 hydrogen bonds · protein-protein
- L–P · 238 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 3UYR · Structure of a monoclonal antibody complexed with its MHC-I antigen · the same entry in another collection · chain H against H, TM-score 1.00
- P01897 · AlphaFold monomer V2.0 prediction for H-2 class I histocompatibility antigen, L-D alpha… · a predicted model of the same protein · chain P against A, TM-score 0.50
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 P01897
- Elsewhere: RCSB PDB 3UYR · PDBe 3UYR · UniProt P01897
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.