Research workbench
Crystal structure of HLA-B8 in complex with qik, a CMV peptide
Analyse Crystal structure of HLA-B8 in complex with qik, a CMV peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WMR
- Type
- protein
- Length
- 376 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, B-8 alpha chain; Beta-2-microglobulin; Qik…
- UniProt
- P30460, P61769
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, B-8 alpha chain | protein | 267 | 27% helix, 40% strand | P30460 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Qik peptide from CMV | protein | 9 | 0% helix, 0% strand | — |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 539 | 0.65 | 0.77 | 52 | empty |
| 2 | 88 | 0.43 | 0.79 | 22 | empty |
| 3 | 75 | 0.39 | 0.78 | 17 | empty |
| 4 | 82 | 0.39 | 0.77 | 16 | empty |
| 5 | 54 | 0.31 | 0.76 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1404 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 943 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
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 P30460
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 5WMR · PDBe 5WMR · UniProt P30460 · UniProt P61769
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