Research workbench
Crystal structure of 9-mer peptide from influenza virus in complex with BF2*1201
Analyse Crystal structure of 9-mer peptide from influenza virus in complex with BF2*1201 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YMV
- Type
- protein
- Length
- 756 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Class I histocompatibility antigen, F10 alpha chain; Beta-2-microglobulin…
- UniProt
- P15979, P21611
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Class I histocompatibility antigen, F10 alpha chain | protein | 271 | 28% helix, 43% strand | P15979 |
| B, E | Beta-2-microglobulin | protein | 98 | 0% helix, 48% strand | P21611 |
| C, F | Ala-val-lys-gly-val-gly-thr-met-val | protein | 9 | 0% helix, 0% strand | — |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1141 | 0.76 | 0.79 | 108 | empty |
| 2 | 705 | 0.72 | 0.78 | 62 | empty |
| 3 | 477 | 0.63 | 0.76 | 52 | empty |
| 4 | 156 | 0.43 | 0.75 | 20 | empty |
| 5 | 62 | 0.41 | 0.81 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1614 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 1593 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 944 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 885 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 884 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5YMV · Crystal structure of 9-mer peptide from influenza virus in complex with BF2*1201 · the same entry in another collection · chain F against F, TM-score 1.00
- P15979 · AlphaFold monomer V2.0 prediction for class I histocompatibility antigen, F10 alpha chain… · a predicted model of the same protein · chain A against A, TM-score 0.98
- P21611 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P21611) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P15979
- Every structure of UniProt P21611
- Elsewhere: RCSB PDB 5YMV · PDBe 5YMV · UniProt P15979 · UniProt P21611
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