Research workbench
Crystal structure of HLA, B*4403, and peptide eeptvikky
Analyse Crystal structure of HLA, B*4403, and peptide eeptvikky in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SYS
- Type
- protein
- Length
- 384 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leukocyte antigen (HLA) class I molecule; Beta-2-microglobulin; Sorting nexin 5
- UniProt
- P30481, P61769, Q9Y5X3
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leukocyte antigen (HLA) class I molecule | protein | 276 | 27% helix, 39% strand | P30481 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | Sorting nexin 5 | protein | 9 | 0% helix, 0% strand | Q9Y5X3 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 625 | 0.68 | 0.77 | 49 | empty |
| 2 | 86 | 0.42 | 0.79 | 19 | empty |
| 3 | 95 | 0.40 | 0.77 | 16 | empty |
| 4 | 73 | 0.38 | 0.78 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1268 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 959 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1SYS · Crystal structure of HLA, B*4403, and peptide EEPTVIKKY · the same entry in another collection · chain A against A, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q9Y5X3 · AlphaFold monomer V2.0 prediction for sorting nexin-5 (Q9Y5X3) · a predicted model of the same protein · chain C against A, TM-score 0.45
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 P30481
- Every structure of UniProt P61769
- Every structure of UniProt Q9Y5X3
- Elsewhere: RCSB PDB 1SYS · PDBe 1SYS · UniProt P30481 · UniProt P61769 · UniProt Q9Y5X3
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