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
- 1S7W
- Type
- protein
- Length
- 1,535 residues
- Chains
- 12
- 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
- 17 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 276 | 25% helix, 38% strand | P01899 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | P01887 |
| C, F, I, L | Glycoprotein 9-residue peptide | protein | 9 | 0% helix, 0% strand | P07399 |
| E, H, K | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P01887 |
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 924 | 0.72 | 0.76 | 100 | empty |
| 2 | 861 | 0.70 | 0.75 | 82 | empty |
| 3 | 749 | 0.68 | 0.76 | 62 | empty |
| 4 | 699 | 0.68 | 0.76 | 60 | empty |
| 5 | 676 | 0.67 | 0.76 | 58 | empty |
Interfaces
12 interfaces between chains.
- G–H · 1290 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1287 Ų buried · 20 hydrogen bonds · protein-protein
- J–K · 1284 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1187 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 990 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 1S7W · Crystal structures of the murine class I major histocompatibility complex H-2Db in… · the same entry in another collection · chain G against G, TM-score 1.00
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 1S7W · PDBe 1S7W · UniProt P01899 · UniProt P01887 · UniProt P07399
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