Research workbench
1.35A crystal structure of H-2KB complexed with the gnysfyal peptide
Analyse 1.35A crystal structure of H-2KB complexed with the gnysfyal peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LK2
- Type
- protein
- Length
- 381 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class I histocompatibility antigen, K-B alpha chain; Beta-2-microglobulin; Insulin…
- UniProt
- P01901, P01887, P15208
- Ligands
- NAG, FUC, PO4
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, K-B alpha chain | protein | 274 | 28% helix, 39% strand | P01901 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 53% strand | P01887 |
| P | Insulin receptor, beta-subunit | protein | 8 | 0% helix, 0% strand | P15208 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · chains A
- PO4 · Phosphate ion · ion · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 250 | 0.59 | 0.79 | 41 | PO4, MRD |
| 2 | 381 | 0.59 | 0.76 | 38 | empty |
| 3 | 64 | 0.52 | 0.86 | 18 | MPD |
| 4 | 113 | 0.48 | 0.80 | 22 | empty |
| 5 | 72 | 0.33 | 0.75 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1346 Ų buried · 23 hydrogen bonds · protein-protein
- A–P · 800 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1LK2 · 1.35A crystal structure of H-2Kb complexed with the GNYSFYAL peptide · the same entry in another collection · chain A against A, TM-score 1.00
- P01901 · AlphaFold monomer V2.0 prediction for H-2 class I histocompatibility antigen, K-B alpha… · a predicted model of the same protein · chain A against A, TM-score 0.99
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain B against A, TM-score 0.97
- P15208 · AlphaFold monomer V2.0 prediction for insulin receptor (P15208) · a predicted model of the same protein · chain P against A, TM-score 0.39
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 P01901
- Every structure of UniProt P01887
- Every structure of UniProt P15208
- Elsewhere: RCSB PDB 1LK2 · PDBe 1LK2 · UniProt P01901 · UniProt P01887 · UniProt P15208
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