Research workbench
HLA-B*15:01 complexed with a synthetic peptide
Analyse HLA-B*15:01 complexed with a synthetic peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UZP
- Type
- protein
- Length
- 385 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.08
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Synthetic peptide…
- UniProt
- A0MSS3, P61769
- Ligands
- NA
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · resolution 2.08 · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 276 | 27% helix, 39% strand | A0MSS3 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Synthetic peptide HIS-LEU-ALA-SER-SER-GLY-HIS-SER-LEU | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, C, B
- ACT · Acetate ion · additive · 2 copies · chains A, B, C
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 617 | 0.70 | 0.78 | 52 | GOL |
| 2 | 85 | 0.56 | 0.86 | 23 | EDO, ACT |
| 3 | 110 | 0.47 | 0.79 | 22 | ACT |
| 4 | 107 | 0.44 | 0.78 | 17 | EDO |
| 5 | 82 | 0.40 | 0.78 | 19 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1325 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 849 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 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 A0MSS3
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6UZP · PDBe 6UZP · UniProt A0MSS3 · UniProt P61769
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