MolNFT v1 · #17803 · protein
Crystal structure of nk receptor LY49C mutant with its MHC class I ligand H-2KB
1P4L · MHC class I H-2KB heavy chain: “Crystal structure of nk receptor LY49C mutant with its MHC class I ligand H-2KB”. X-ray diffraction, 6 pockets (best druggability 0.85). MolNFT v1 #17803 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1P4L
- Type
- protein
- Length
- 502 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I H-2KB heavy chain; Beta-2-microglobulin; Ovalbumin peptide; LY49-C
- UniProt
- P01901, P01887, P01012, Q64329
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I H-2KB heavy chain | protein | 273 | 25% helix, 39% strand | P01901 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 40% strand | P01887 |
| P | Ovalbumin peptide | protein | 8 | 0% helix, 0% strand | P01012 |
| D | LY49-C | protein | 122 | 16% helix, 34% strand | Q64329 |
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1036 | 0.85 | 0.86 | 95 | empty |
| 2 | 216 | 0.64 | 0.83 | 31 | empty |
| 3 | 215 | 0.57 | 0.79 | 29 | empty |
| 4 | 219 | 0.55 | 0.78 | 38 | empty |
| 5 | 180 | 0.54 | 0.79 | 30 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1242 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1096 Ų buried · 13 hydrogen bonds · protein-protein
- A–P · 819 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 352 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 1P4L · Crystal structure of NK receptor Ly49C mutant with its MHC class I ligand H-2Kb · the same entry in another collection · chain A against A, TM-score 1.00
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q64329 · AlphaFold monomer V2.0 prediction for killer cell lectin-like receptor 3 (Q64329) · a predicted model of the same protein · chain D against A, TM-score 0.93
- P01012 · AlphaFold monomer V2.0 prediction for ovalbumin (P01012) · a predicted model of the same protein · chain P against A, TM-score 0.46
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 P01901
- Every structure of UniProt P01887
- Every structure of UniProt P01012
- Every structure of UniProt Q64329
- Elsewhere: RCSB PDB 1P4L · PDBe 1P4L · UniProt P01901 · UniProt P01887 · UniProt P01012 · UniProt Q64329
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