Research workbench
MHC class I H-2DD heavy chain complexed with beta-2 microglobulin and an immunodominant peptide P18-I10 from the human immunodeficiency virus envelope glycoprotein 120
Analyse MHC class I H-2DD heavy chain complexed with beta-2 microglobulin and an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DDH
- Type
- protein
- Length
- 383 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I H-2DD heavy chain; Beta-2 microglobulin; Human immunodeficiency virus…
- UniProt
- P01900, P01887, P04582
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I H-2DD heavy chain | protein | 274 | 26% helix, 38% strand | P01900 |
| B | Beta-2 microglobulin | protein | 99 | 0% helix, 46% strand | P01887 |
| P | Human immunodeficiency virus envelope glycoprotein 120 | protein | 10 | 0% helix, 0% strand | P04582 |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 713 | 0.70 | 0.77 | 56 | empty |
| 2 | 103 | 0.51 | 0.82 | 22 | empty |
| 3 | 146 | 0.42 | 0.75 | 30 | empty |
| 4 | 58 | 0.34 | 0.77 | 14 | empty |
| 5 | 51 | 0.30 | 0.76 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1284 Ų buried · 19 hydrogen bonds · protein-protein
- A–P · 953 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1DDH · MHC class I H-2DD heavy chain complexed with beta-2 microglobulin and an immunodominant… · the same entry in another collection · chain A against A, 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 0.97
- 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 0.92
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 P01887
- Every structure of UniProt P04582
- Elsewhere: RCSB PDB 1DDH · PDBe 1DDH · UniProt P01900 · UniProt P01887 · UniProt P04582
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