Research workbench
HLA-B*07:02 in complex with SARS-CoV-2 nucleocapsid peptide N105-113
Analyse HLA-B*07:02 in complex with SARS-CoV-2 nucleocapsid peptide N105-113 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LGD
- Type
- protein
- Length
- 770 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.88
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- HLA class I histocompatibility antigen, B alpha chain; Beta-2-microglobulin; SARS-CoV-2…
- UniProt
- P01889, P61769, P0DTC9
- Ligands
- NA, CL, SO4
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · resolution 2.88 · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | HLA class I histocompatibility antigen, B alpha chain | protein | 276 | 26% helix, 40% strand | P01889 |
| B, D | Beta-2-microglobulin | protein | 100 | 0% helix, 47% strand | P61769 |
| E, F | SARS-CoV-2 nucleocapsid peptide N105-113 | protein | 9 | 0% helix, 0% strand | P0DTC9 |
Ligands and binding sites
- NA · Sodium ion · metal
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains C, 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 | 536 | 0.69 | 0.79 | 51 | empty |
| 2 | 550 | 0.69 | 0.79 | 56 | empty |
| 3 | 297 | 0.57 | 0.77 | 33 | empty |
| 4 | 153 | 0.54 | 0.81 | 28 | empty |
| 5 | 185 | 0.49 | 0.77 | 35 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1360 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1342 Ų buried · 23 hydrogen bonds · protein-protein
- C–E · 1015 Ų buried · 18 hydrogen bonds · protein-protein
- A–F · 1006 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 313 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 7LGD · HLA-B*07:02 in complex with SARS-cov-2 nucleocapsid peptide N105-113 · the same entry in another collection · chain F against F, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain D against A, TM-score 0.99
- P01889 · AlphaFold monomer V2.0 prediction for HLA class I histocompatibility antigen, B alpha… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P01889
- Every structure of UniProt P61769
- Every structure of UniProt P0DTC9
- Elsewhere: RCSB PDB 7LGD · PDBe 7LGD · UniProt P01889 · UniProt P61769 · UniProt P0DTC9
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