Research workbench
Crystal structure of HLA-A*2402 complexed with 4-mer lipopeptide
Analyse Crystal structure of HLA-A*2402 complexed with 4-mer lipopeptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WT3
- Type
- protein
- Length
- 677 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; 4-mer lipopeptide
- UniProt
- A0A411J078, P61769
- Ligands
- MYR, ZN
- Pockets
- 12 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 21% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 277 | 27% helix, 40% strand | A0A411J078 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, F | 4-mer lipopeptide | protein | 4 | 0% helix, 0% strand | — |
| D | MHC class I antigen | protein | 210 | 32% helix, 30% strand | A0A411J078 |
| E | Beta-2-microglobulin | protein | 82 | 0% helix, 48% strand | P61769 |
Ligands and binding sites
- MYR · Myristic acid · ligand · 2 copies · chains A, C, D, F
- ZN · Zinc ion · metal · 3 copies · chains A, D
- EDO · 1,2-ethanediol · additive · 37 copies · chains A, B, D, E
- ACT · Acetate ion · additive · 3 copies · chains A, D, E
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 703 | 0.71 | 0.78 | 62 | ACT, EDO |
| 2 | 266 | 0.67 | 0.83 | 33 | MYR |
| 3 | 257 | 0.66 | 0.83 | 32 | MYR, EDO |
| 4 | 516 | 0.63 | 0.76 | 53 | ACT, EDO |
| 5 | 116 | 0.44 | 0.78 | 23 | EDO |
Interfaces
4 interfaces between chains.
- A–B · 1294 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1024 Ų buried · 20 hydrogen bonds · protein-protein
- D–F · 420 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 390 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 lipid (disulfide, myristoylation).
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 A0A411J078
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 7WT3 · PDBe 7WT3 · UniProt A0A411J078 · UniProt P61769
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