Research workbench
Crystal structures of the murine class I major histocompatibility complex H-2DB in complex with lcmv-derived GP33 index peptide and three of its escape variants
Analyse Crystal structures of the murine class I major histocompatibility complex H-2DB… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1S7V
- 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…
- UniProt
- P01899, P01887, P07399
- Pockets
- 11 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 276 | 26% helix, 39% strand | P01899 |
| B, E | Beta-2-microglobulin | protein | 99 | 0% helix, 47% strand | P01887 |
| C, F | Glycoprotein 9-residue peptide | protein | 9 | 0% helix, 0% strand | P07399 |
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 425 | 0.66 | 0.79 | 43 | empty |
| 2 | 382 | 0.64 | 0.78 | 41 | empty |
| 3 | 103 | 0.44 | 0.78 | 23 | empty |
| 4 | 115 | 0.43 | 0.77 | 22 | empty |
| 5 | 60 | 0.42 | 0.82 | 17 | empty |
Interfaces
4 interfaces between chains.
- D–E · 1413 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1401 Ų buried · 27 hydrogen bonds · protein-protein
- D–F · 909 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 905 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1S7V · Crystal structures of the murine class I major histocompatibility complex H-2Db in… · the same entry in another collection · chain C against C, TM-score 1.00
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain E 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 P01899
- Every structure of UniProt P01887
- Every structure of UniProt P07399
- Elsewhere: RCSB PDB 1S7V · PDBe 1S7V · UniProt P01899 · UniProt P01887 · UniProt P07399
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