Research workbench
Crystal structure of HLA-B7 in complex with spi, an influenza peptide
Analyse Crystal structure of HLA-B7 in complex with spi, an influenza peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WMN
- Type
- protein
- Length
- 769 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, B-7 alpha chain; Beta-2-microglobulin; Spi…
- UniProt
- P01889, P61769
- Pockets
- 8 · best druggability 0.76
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-7 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 | 100 | 0% helix, 49% strand | P61769 |
| E, F | Spi peptide from influenza a virus | protein | 9 | 0% helix, 0% strand | — |
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 828 | 0.76 | 0.80 | 77 | empty |
| 2 | 622 | 0.71 | 0.79 | 55 | empty |
| 3 | 209 | 0.49 | 0.76 | 32 | empty |
| 4 | 183 | 0.48 | 0.76 | 29 | empty |
| 5 | 70 | 0.43 | 0.81 | 19 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1399 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1335 Ų buried · 25 hydrogen bonds · protein-protein
- A–E · 922 Ų buried · 17 hydrogen bonds · protein-protein
- C–F · 922 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 526 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5WMN · Crystal Structure of HLA-B7 in complex with SPI, an influenza peptide · the same entry in another collection · chain F against F, TM-score 1.00
- 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 0.99
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.99
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
- Elsewhere: RCSB PDB 5WMN · PDBe 5WMN · UniProt P01889 · UniProt P61769
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