Research workbench
MHC class I H-2KB presented glycopeptide RGY8-6H-GAL2
Analyse MHC class I H-2KB presented glycopeptide RGY8-6H-GAL2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KBG
- Type
- protein
- Length
- 381 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (major histocompatibility complex class I antigen H-2KB); Protein…
- UniProt
- P01901, P01887, P11212
- Ligands
- NAG, FUC, GAL, GLA
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Protein (major histocompatibility complex class I antigen H-2KB) | protein | 274 | 28% helix, 40% strand | P01901 |
| L | Protein (beta-2-microglobulin) | protein | 99 | 0% helix, 53% strand | P01887 |
| P | Protein (synthetic glycopeptide RGY8-6H-GAL2) | protein | 8 | 0% helix, 0% strand | P11212 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains H
- FUC · alpha-L-fucopyranose · sugar · chains H
- GAL · beta-D-galactopyranose · sugar · chains H, P
- GLA · alpha-D-galactopyranose · sugar · chains H
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 | 207 | 0.59 | 0.81 | 34 | empty |
| 2 | 122 | 0.54 | 0.82 | 24 | empty |
| 3 | 251 | 0.52 | 0.75 | 28 | empty |
| 4 | 123 | 0.48 | 0.79 | 21 | empty |
| 5 | 81 | 0.35 | 0.75 | 16 | empty |
Interfaces
2 interfaces between chains.
- H–L · 1374 Ų buried · 26 hydrogen bonds · protein-protein
- H–P · 949 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 glycan, 1 modified (disulfide, N-glycosylation, glycosylation, nonstandard).
Compared structures
- 1KBG · MHC Class I H-2KB Presented Glycopeptide RGY8-6H-GAL2 · the same entry in another collection · chain H against H, 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 H 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 L against A, TM-score 0.96
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 P11212
- Elsewhere: RCSB PDB 1KBG · PDBe 1KBG · UniProt P01901 · UniProt P01887 · UniProt P11212
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