MolNFT v1 · #180984 · protein
HLA-B*07:02 in complex with 229E-derived coronavirus nucleocapsid peptide N75-83
7LGT · HLA class I histocompatibility antigen, B alpha chain: “HLA-B*07:02 in complex with 229E-derived coronavirus nucleocapsid peptide N75-83”. X-ray diffraction, 5 ligands (K, ZN, NA), 5 pockets (best druggability 0.77). MolNFT v1…
- PDB
- 7LGT
- Type
- protein
- Length
- 767 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, B alpha chain; Beta-2-microglobulin…
- UniProt
- P01889, P61769, P15130
- Ligands
- K, ZN, NA, CL, BR
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | HLA class I histocompatibility antigen, B alpha chain | protein | 276 | 27% helix, 39% strand | P01889 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| D | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | P61769 |
| E, F | Nucleoprotein peptide N75-83 | protein | 9 | 0% helix, 0% strand | P15130 |
Ligands and binding sites
- K · Potassium ion · metal · 12 copies · chains A, F, B, C, D
- ZN · Zinc ion · metal · 11 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, C, D
- CL · Chloride ion · ion · 9 copies · chains A, B, F, C
- BR · Bromide ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1159 | 0.77 | 0.79 | 117 | K |
| 2 | 492 | 0.68 | 0.79 | 47 | K |
| 3 | 155 | 0.55 | 0.81 | 26 | empty |
| 4 | 164 | 0.52 | 0.79 | 23 | CL |
| 5 | 84 | 0.38 | 0.77 | 21 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1381 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1346 Ų buried · 24 hydrogen bonds · protein-protein
- A–F · 935 Ų buried · 19 hydrogen bonds · protein-protein
- C–E · 904 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 314 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 7LGT · HLA-B*07:02 in complex with 229E-derived coronavirus nucleocapsid peptide N75-83 · 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 B against A, TM-score 0.98
- 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 P15130
- Elsewhere: RCSB PDB 7LGT · PDBe 7LGT · UniProt P01889 · UniProt P61769 · UniProt P15130
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