MolNFT v1 · #36487 · protein
Murine MHC class I H-2DB in complex with human B2-microglobulin and lcmv-derived immunodminant peptide GP33
2F74 · H-2 class I histocompatibility antigen, D-B alpha chain: “Murine MHC class I H-2DB in complex with human B2-microglobulin and lcmv-derived immunodminant peptide GP33”. X-ray diffraction, 6 pockets (best druggability 0.65). MolNFT v1…
- PDB
- 2F74
- Type
- protein
- Length
- 768 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; Nonameric…
- UniProt
- P01899, P61769
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 5 distinct chains · 18% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 275 | 25% helix, 41% strand | P01899 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, F | Nonameric peptide, GP33, derived from lymphocytic choriomeningitis virus | protein | 9 | 0% helix, 0% strand | — |
| D | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 276 | 25% helix, 42% strand | P01899 |
| E | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
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 | 614 | 0.65 | 0.75 | 55 | empty |
| 2 | 343 | 0.64 | 0.80 | 38 | empty |
| 3 | 591 | 0.64 | 0.75 | 55 | empty |
| 4 | 72 | 0.35 | 0.76 | 17 | empty |
| 5 | 80 | 0.35 | 0.76 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1428 Ų buried · 24 hydrogen bonds · protein-protein
- D–E · 1356 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 929 Ų buried · 26 hydrogen bonds · protein-protein
- D–F · 908 Ų buried · 25 hydrogen bonds · protein-protein
- A–E · 304 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2F74 · Murine MHC class I H-2Db in complex with human b2-microglobulin and LCMV-derived… · the same entry in another collection · chain F against F, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain E against A, TM-score 0.98
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
- Elsewhere: RCSB PDB 2F74 · PDBe 2F74 · UniProt P01899 · UniProt P61769
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