Research workbench
Crystal structure of MHC-I like protein
Analyse Crystal structure of MHC-I like protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BMK
- Type
- protein
- Length
- 740 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antigen-presenting glycoprotein CD1D2; Beta-2-microglobulin
- UniProt
- P11610, P01887
- Ligands
- F57, NAG
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Antigen-presenting glycoprotein CD1D2 | protein | 272 | 27% helix, 42% strand | P11610 |
| B, D | Beta-2-microglobulin | protein | 98 | 0% helix, 48% strand | P01887 |
Ligands and binding sites
- F57 · (2R)-1-(decanoyloxy)-3-(phosphonooxy)propan-2-yl octadecanoate · ligand · 2 copies · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 407 | 0.83 | 0.90 | 51 | F57 |
| 2 | 407 | 0.83 | 0.90 | 52 | F57 |
| 3 | 440 | 0.64 | 0.78 | 63 | empty |
| 4 | 307 | 0.61 | 0.78 | 45 | empty |
| 5 | 166 | 0.48 | 0.76 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1286 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1286 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 249 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6BMK · Crystal structure of MHC-I like protein · the same entry in another collection · chain D against D, TM-score 1.00
- P11610 · AlphaFold monomer V2.0 prediction for antigen-presenting glycoprotein CD1D2 (P11610) · a predicted model of the same protein · chain C against A, TM-score 0.98
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P11610
- Every structure of UniProt P01887
- Elsewhere: RCSB PDB 6BMK · PDBe 6BMK · UniProt P11610 · UniProt P01887
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