MolNFT v1 · #135457 · protein
Structure of the viral immunoevasin M12 (smith) bound to the natural killer cell receptor nkr-P1B (B6)
5TZN · Killer cell lectin-like receptor subfamily B member 1B…: “Structure of the viral immunoevasin M12 (smith) bound to the natural killer cell receptor nkr-P1B (B6)”. X-ray diffraction, 4 ligands (NAG, FUC, BMA), 7 pockets (best…
- PDB
- 5TZN
- Type
- protein
- Length
- 525 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Killer cell lectin-like receptor subfamily B member 1B allele B; Glycoprotein family…
- UniProt
- Q99JB4, D3XDJ6
- Ligands
- NAG, FUC, BMA, IOD
- Pockets
- 7 · best druggability 0.54
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Killer cell lectin-like receptor subfamily B member 1B allele B | protein | 124 | 15% helix, 36% strand | Q99JB4 |
| F | Glycoprotein family protein M12 | protein | 137 | 3% helix, 42% strand | D3XDJ6 |
| G | Glycoprotein family protein M12 | protein | 144 | 3% helix, 40% strand | D3XDJ6 |
| W | Killer cell lectin-like receptor subfamily B member 1B allele B | protein | 120 | 16% helix, 38% strand | Q99JB4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, F, G, W
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains F, G
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, G
- IOD · Iodide ion · ion · 2 copies · chains A, F, G, W
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 316 | 0.54 | 0.75 | 44 | empty |
| 2 | 105 | 0.44 | 0.78 | 19 | empty |
| 3 | 123 | 0.42 | 0.76 | 28 | empty |
| 4 | 125 | 0.41 | 0.75 | 24 | empty |
| 5 | 52 | 0.35 | 0.79 | 13 | empty |
Interfaces
5 interfaces between chains.
- G–W · 1133 Ų buried · 23 hydrogen bonds · protein-protein
- A–F · 1089 Ų buried · 22 hydrogen bonds · protein-protein
- A–G · 480 Ų buried · 7 hydrogen bonds · protein-protein
- F–G · 407 Ų buried · 5 hydrogen bonds · protein-protein
- F–W · 350 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 5TZN · Structure of the viral immunoevasin m12 (Smith) bound to the natural killer cell receptor… · the same entry in another collection · chain A against A, TM-score 1.00
- Q99JB4 · AlphaFold monomer V2.0 prediction for killer cell lectin-like receptor subfamily B member… · a predicted model of the same protein · chain W against A, TM-score 0.93
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 Q99JB4
- Every structure of UniProt D3XDJ6
- Elsewhere: RCSB PDB 5TZN · PDBe 5TZN · UniProt Q99JB4 · UniProt D3XDJ6
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