MolNFT v1 · #60807 · protein
Structure of UL18, a peptide-binding viral MHC mimic, bound to a host inhibitory receptor
3D2U · UL18 protein: “Structure of UL18, a peptide-binding viral MHC mimic, bound to a host inhibitory receptor”. X-ray diffraction, 4 ligands (NAG, MAN, BMA), 9 pockets (best druggability 0.74). MolNFT v1 #60807 on GenesisL1: 3D…
- PDB
- 3D2U
- Type
- protein
- Length
- 1,143 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UL18 protein; Beta-2-microglobulin; Leukocyte immunoglobulin-like receptor subfamily B…
- UniProt
- Q4A1U8, P61769, Q8NHL6, P60709
- Ligands
- NAG, MAN, BMA, FUC
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 6 distinct chains · 16% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UL18 protein | protein | 281 | 26% helix, 42% strand | Q4A1U8 |
| B, F | Beta-2-microglobulin | protein | 99 | 0% helix, 52% strand | P61769 |
| D | Leukocyte immunoglobulin-like receptor subfamily B member 1 | protein | 182 | 7% helix, 46% strand | Q8NHL6 |
| E | UL18 protein | protein | 279 | 26% helix, 42% strand | Q4A1U8 |
| H | Leukocyte immunoglobulin-like receptor subfamily B member 1 | protein | 185 | 6% helix, 46% strand | Q8NHL6 |
| G, C | Actin | protein | 9 | 0% helix, 0% strand | P60709 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, C, E
- MAN · alpha-D-mannopyranose · sugar · chains F
- BMA · beta-D-mannopyranose · sugar · chains F
- FUC · alpha-L-fucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 875 | 0.74 | 0.78 | 61 | empty |
| 2 | 916 | 0.74 | 0.78 | 64 | empty |
| 3 | 287 | 0.62 | 0.80 | 34 | empty |
| 4 | 203 | 0.60 | 0.81 | 28 | empty |
| 5 | 208 | 0.45 | 0.73 | 25 | empty |
Interfaces
9 interfaces between chains.
- E–F · 1544 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1520 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 910 Ų buried · 9 hydrogen bonds · protein-protein
- E–G · 899 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 644 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 3D2U · Structure of UL18, a Peptide-Binding Viral MHC Mimic, Bound to a Host Inhibitory Receptor · the same entry in another collection · chain C against C, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain F against A, TM-score 0.98
- Q8NHL6 · AlphaFold monomer V2.0 prediction for leukocyte immunoglobulin-like receptor subfamily B… · a predicted model of the same protein · chain D against A, TM-score 0.95
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 Q4A1U8
- Every structure of UniProt P61769
- Every structure of UniProt Q8NHL6
- Every structure of UniProt P60709
- Elsewhere: RCSB PDB 3D2U · PDBe 3D2U · UniProt Q4A1U8 · UniProt P61769 · UniProt Q8NHL6 · UniProt P60709
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