Research workbench
Peptide-MHC complex of mouse H2-db presenting PA224 with E4C mutation
Analyse Peptide-MHC complex of mouse H2-db presenting PA224 with E4C mutation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7N5Q
- Type
- protein
- Length
- 777 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; Peptide…
- UniProt
- P01899, P61769, O89752
- Ligands
- NA
- Pockets
- 11 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 279 | 28% helix, 38% strand | P01899 |
| B, G | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, H | Peptide from polymerase acidic protein | protein | 10 | 0% helix, 0% strand | O89752 |
| F | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 278 | 27% helix, 37% strand | P01899 |
Ligands and binding sites
- NA · Sodium ion · metal · 11 copies · chains A, C, B, F, G
- ACT · Acetate ion · additive · 3 copies · chains A, B, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 564 | 0.72 | 0.80 | 64 | NA |
| 2 | 244 | 0.62 | 0.81 | 34 | empty |
| 3 | 178 | 0.55 | 0.80 | 24 | empty |
| 4 | 120 | 0.54 | 0.83 | 27 | empty |
| 5 | 61 | 0.44 | 0.82 | 16 | NA, ACT |
Interfaces
7 interfaces between chains.
- A–B · 1390 Ų buried · 23 hydrogen bonds · protein-protein
- F–G · 1268 Ų buried · 22 hydrogen bonds · protein-protein
- F–H · 895 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 893 Ų buried · 27 hydrogen bonds · protein-protein
- A–F · 534 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7N5Q · Peptide-MHC complex of mouse H2-Db presenting PA224 with E4C mutation · the same entry in another collection · chain H against H, 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 0.99
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 P61769
- Every structure of UniProt O89752
- Elsewhere: RCSB PDB 7N5Q · PDBe 7N5Q · UniProt P01899 · UniProt P61769 · UniProt O89752
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