Research workbench
A2 HLA complex with G4A heteroclitic variant of melanoma peptide
Analyse A2 HLA complex with G4A heteroclitic variant of melanoma peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JFP
- Type
- protein
- Length
- 772 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a-2 alpha chain; Beta-2-microglobulin; G4A…
- UniProt
- P01892, P61769
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 276 | 26% helix, 40% strand | P01892 |
| B, E | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, F | G4A heteroclitic melanoma peptide | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B, D, E
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, D, E
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 715 | 0.71 | 0.77 | 59 | EDO |
| 2 | 674 | 0.69 | 0.77 | 53 | SO4 |
| 3 | 119 | 0.45 | 0.78 | 26 | empty |
| 4 | 96 | 0.42 | 0.78 | 19 | empty |
| 5 | 82 | 0.39 | 0.78 | 17 | EDO |
Interfaces
7 interfaces between chains.
- A–B · 1442 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 1396 Ų buried · 26 hydrogen bonds · protein-protein
- D–F · 900 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 896 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 87 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
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 P01892
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 4JFP · PDBe 4JFP · UniProt P01892 · UniProt P61769
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