Research workbench
MHC class I H-2DD heavy chain complexed with beta-2 microglobulin and a variant peptide, PA9, from the human immunodeficiency virus (bal) envelope glycoprotein 120
Analyse MHC class I H-2DD heavy chain complexed with beta-2 microglobulin and a variant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3E6F
- Type
- protein
- Length
- 381 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class I histocompatibility antigen, D-D alpha chain; Beta-2 microglobulin; Envelope…
- UniProt
- P01900, Q91XJ8, Q9YZ87
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, D-D alpha chain | protein | 273 | 26% helix, 41% strand | P01900 |
| B | Beta-2 microglobulin | protein | 99 | 0% helix, 49% strand | Q91XJ8 |
| P | Envelope glycoprotein 9-residue peptide | protein | 9 | 0% helix, 0% strand | Q9YZ87 |
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 570 | 0.68 | 0.78 | 54 | empty |
| 2 | 76 | 0.52 | 0.85 | 18 | empty |
| 3 | 148 | 0.50 | 0.79 | 24 | empty |
| 4 | 50 | 0.30 | 0.76 | 13 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1336 Ų buried · 17 hydrogen bonds · protein-protein
- A–P · 850 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3E6F · MHC CLASS I H-2Dd Heavy chain complexed with Beta-2 Microglobulin and a variant peptide… · the same entry in another collection · chain A against A, TM-score 1.00
- P01900 · AlphaFold monomer V2.0 prediction for H-2 class I histocompatibility antigen, D-D alpha… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P01900
- Every structure of UniProt Q91XJ8
- Every structure of UniProt Q9YZ87
- Elsewhere: RCSB PDB 3E6F · PDBe 3E6F · UniProt P01900 · UniProt Q91XJ8 · UniProt Q9YZ87
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