Research workbench
Crystal structure of HLA-A1:MAGE-A1 in complex with Fab- HYB3
Analyse Crystal structure of HLA-A1:MAGE-A1 in complex with Fab- HYB3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1W72
- Type
- protein
- Length
- 1,632 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen; Beta-2-microglobulin; Melanoma-associated antigen…
- UniProt
- P30443, P61769, P43355
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 13% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | HLA class I histocompatibility antigen | protein | 274 | 27% helix, 42% strand | P30443 |
| B, E | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, F | Melanoma-associated antigen 1 | protein | 9 | 0% helix, 0% strand | P43355 |
| H, I | HYB3 heavy chain | protein | 223 | 5% helix, 49% strand | — |
| L, M | HYB3 light chain | protein | 210 | 8% helix, 50% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains A, I, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 785 | 0.75 | 0.80 | 78 | empty |
| 2 | 637 | 0.68 | 0.77 | 60 | GOL |
| 3 | 604 | 0.68 | 0.77 | 60 | empty |
| 4 | 273 | 0.65 | 0.82 | 31 | empty |
| 5 | 262 | 0.61 | 0.80 | 25 | empty |
Interfaces
18 interfaces between chains.
- I–M · 1850 Ų buried · 16 hydrogen bonds · protein-protein
- H–L · 1747 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1398 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1379 Ų buried · 31 hydrogen bonds · protein-protein
- D–F · 855 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 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 P30443
- Every structure of UniProt P61769
- Every structure of UniProt P43355
- Elsewhere: RCSB PDB 1W72 · PDBe 1W72 · UniProt P30443 · UniProt P61769 · UniProt P43355
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