MolNFT v1 · #96301 · protein
A2 HLA complex with L8A heteroclitic variant of melanoma peptide
4JFQ · HLA class I histocompatibility antigen, a-2 alpha chain: “A2 HLA complex with L8A heteroclitic variant of melanoma peptide”. X-ray diffraction, 8 pockets (best druggability 0.77). MolNFT v1 #96301 on GenesisL1: 3D structure, binding…
- PDB
- 4JFQ
- Type
- protein
- Length
- 771 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; L8A…
- UniProt
- P01892, P61769
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 275 | 28% helix, 40% strand | P01892 |
| B, E | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, F | L8A heteroclitic melanoma peptide | protein | 10 | 0% helix, 0% strand | — |
| D | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 276 | 27% helix, 39% strand | P01892 |
Ligands and binding sites
- GOL · Glycerol · additive · 19 copies · chains A, D, B, E
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1146 | 0.77 | 0.79 | 102 | GOL |
| 2 | 815 | 0.73 | 0.78 | 80 | GOL |
| 3 | 175 | 0.54 | 0.79 | 31 | GOL |
| 4 | 173 | 0.53 | 0.79 | 32 | GOL |
| 5 | 139 | 0.46 | 0.77 | 24 | empty |
Interfaces
5 interfaces between chains.
- D–E · 1433 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1427 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 848 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 841 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 624 Ų buried · 13 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 4JFQ · PDBe 4JFQ · UniProt P01892 · UniProt P61769
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