Research workbench
Crystal structure of class II MHC molecule iab bound to EALPHA3K peptide
Analyse Crystal structure of class II MHC molecule iab bound to EALPHA3K peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LNU
- Type
- protein
- Length
- 1,596 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class II histocompatibility antigen, a-B alpha chain; H-2 class II histocompatibility…
- UniProt
- P14434, P14483
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | H-2 class II histocompatibility antigen, a-B alpha chain | protein | 182 | 15% helix, 42% strand | P14434 |
| B, D, F, H | H-2 class II histocompatibility antigen, a beta chain | protein | 217 | 16% helix, 36% strand | P14483 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 947 | 0.74 | 0.78 | 69 | empty |
| 2 | 938 | 0.74 | 0.77 | 71 | empty |
| 3 | 70 | 0.73 | 0.97 | 20 | empty |
| 4 | 396 | 0.57 | 0.74 | 30 | empty |
| 5 | 266 | 0.52 | 0.75 | 31 | empty |
Interfaces
9 interfaces between chains.
- C–D · 3311 Ų buried · 61 hydrogen bonds · protein-protein
- E–F · 3304 Ų buried · 58 hydrogen bonds · protein-protein
- G–H · 3290 Ų buried · 58 hydrogen bonds · protein-protein
- A–B · 3284 Ų buried · 60 hydrogen bonds · protein-protein
- D–F · 750 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 1LNU · CRYSTAL STRUCTURE OF CLASS II MHC MOLECULE IAb BOUND TO EALPHA3K PEPTIDE · the same entry in another collection · chain H against H, TM-score 1.00
- P14434 · AlphaFold monomer V2.0 prediction for H-2 class II histocompatibility antigen, a-B alpha… · a predicted model of the same protein · chain A against A, TM-score 0.94
- P14483 · AlphaFold monomer V2.0 prediction for H-2 class II histocompatibility antigen, a beta… · a predicted model of the same protein · chain B against A, TM-score 0.68
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 P14434
- Every structure of UniProt P14483
- Elsewhere: RCSB PDB 1LNU · PDBe 1LNU · UniProt P14434 · UniProt P14483
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.