MolNFT v1 · #12512 · protein
Murine alloreactive scfv TCR-peptide-MHC class I molecule complex
1KJ2 · Allogeneic H-2KB MHC class I molecule: “Murine alloreactive scfv TCR-peptide-MHC class I molecule complex”. X-ray diffraction, 4 ligands (NAG, MAN, GAL), 17 pockets (best druggability 0.79). MolNFT v1 #12512 on GenesisL1: 3D…
- PDB
- 1KJ2
- Type
- protein
- Length
- 1,223 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Allogeneic H-2KB MHC class I molecule; Naturally processed octapeptide PKB1; Beta-2…
- UniProt
- O08582, P01887
- Ligands
- NAG, MAN, GAL, SIA
- Pockets
- 17 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 17% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Allogeneic H-2KB MHC class I molecule | protein | 276 | 27% helix, 40% strand | — |
| P, Q | Naturally processed octapeptide PKB1 | protein | 8 | 0% helix, 0% strand | O08582 |
| L, M | Beta-2 microglobulin | protein | 99 | 0% helix, 47% strand | P01887 |
| A, D | KB5-C20 T-cell receptor alpha-chain | protein | 111 | 0% helix, 59% strand | — |
| B, E | KB5-C20 T-cell receptor beta-chain | protein | 117 | 0% helix, 54% strand | — |
| I | Allogeneic H-2KB MHC class I molecule | protein | 277 | 26% helix, 39% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B, E
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- GAL · beta-D-galactopyranose · sugar · chains A
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 810 | 0.79 | 0.82 | 82 | empty |
| 2 | 832 | 0.77 | 0.81 | 77 | empty |
| 3 | 643 | 0.67 | 0.76 | 55 | empty |
| 4 | 487 | 0.60 | 0.74 | 43 | empty |
| 5 | 98 | 0.43 | 0.78 | 25 | empty |
Interfaces
17 interfaces between chains.
- I–M · 1293 Ų buried · 22 hydrogen bonds · protein-protein
- H–L · 1191 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 930 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 926 Ų buried · 15 hydrogen bonds · protein-protein
- H–P · 908 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 3 glycan (disulfide, N-glycosylation).
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 O08582
- Every structure of UniProt P01887
- Elsewhere: RCSB PDB 1KJ2 · PDBe 1KJ2 · UniProt O08582 · UniProt P01887
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