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Structure of the hcmv UL16-micb complex elucidates select binding of a viral immunoevasin to diverse NKG2D ligands
Analyse Structure of the hcmv UL16-micb complex elucidates select binding of a viral… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WY3
- Type
- protein
- Length
- 610 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I polypeptide-related sequence B; Uncharacterized protein UL16
- UniProt
- Q29980, P16757
- Ligands
- PEU, NAG
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I polypeptide-related sequence B | protein | 173 | 37% helix, 35% strand | Q29980 |
| B | Uncharacterized protein UL16 | protein | 137 | 4% helix, 55% strand | P16757 |
| C | MHC class I polypeptide-related sequence B | protein | 167 | 37% helix, 36% strand | Q29980 |
| D | Uncharacterized protein UL16 | protein | 133 | 5% helix, 56% strand | P16757 |
Ligands and binding sites
- PEU · 2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56, 59,62,65,68,71,74,77,80-heptacosaoxadooctacontan-82-ol · ligand · 3 copies · chains A, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains B, D
- ACT · Acetate ion · additive · 3 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 367 | 0.72 | 0.84 | 39 | empty |
| 2 | 319 | 0.69 | 0.83 | 42 | empty |
| 3 | 624 | 0.64 | 0.75 | 51 | PEU |
| 4 | 189 | 0.54 | 0.79 | 23 | empty |
| 5 | 179 | 0.52 | 0.78 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1159 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 922 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 358 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 glycan, 6 disulfide (N-glycosylation, disulfide).
Compared structures
- 2WY3 · Structure of the HCMV UL16-MICB complex elucidates select binding of a viral immunoevasin… · the same entry in another collection · chain A against A, TM-score 1.00
- Q29980 · AlphaFold monomer V2.0 prediction for MHC class I polypeptide-related sequence B (Q29980) · a predicted model of the same protein · chain A 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 Q29980
- Every structure of UniProt P16757
- Elsewhere: RCSB PDB 2WY3 · PDBe 2WY3 · UniProt Q29980 · UniProt P16757
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