Research workbench
Crystal structure of H-2DB in complex with a variant M6A of the NP366 peptide from influenza a virus
Analyse Crystal structure of H-2DB in complex with a variant M6A of the NP366 peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CPL
- Type
- protein
- Length
- 766 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class I histocompatibility antigen, D-B alpha chain; Beta-2-microglobulin; NP366…
- UniProt
- P01899, P01887
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 275 | 25% helix, 39% strand | P01899 |
| B, D | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P01887 |
| E, F | NP366 peptide | protein | 9 | 0% helix, 0% strand | — |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 645 | 0.76 | 0.82 | 70 | empty |
| 2 | 607 | 0.65 | 0.75 | 60 | empty |
| 3 | 581 | 0.63 | 0.74 | 56 | empty |
| 4 | 108 | 0.48 | 0.80 | 18 | empty |
| 5 | 123 | 0.45 | 0.77 | 20 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1273 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1273 Ų buried · 21 hydrogen bonds · protein-protein
- C–F · 880 Ų buried · 26 hydrogen bonds · protein-protein
- A–E · 878 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 299 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3CPL · Crystal Structure of H-2Db in complex with a variant M6A of the NP366 peptide from… · the same entry in another collection · chain F against F, TM-score 1.00
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · 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 P01899
- Every structure of UniProt P01887
- Elsewhere: RCSB PDB 3CPL · PDBe 3CPL · UniProt P01899 · UniProt P01887
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