Research workbench
Crystal structures of the murine class I major histocompatibility complex H-2DB in complex with adenovirus-derived peptide AD10
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
- 6H6D
- Type
- protein
- Length
- 763 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; Early E1A…
- UniProt
- P01899, P01887, P03255
- Ligands
- CL, SO4
- Pockets
- 12 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 272 | 25% helix, 39% strand | P01899 |
| B, E | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P01887 |
| C, F | Early E1A protein | protein | 10 | 0% helix, 0% strand | P03255 |
| D | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 273 | 25% helix, 39% strand | P01899 |
Ligands and binding sites
- CL · Chloride ion · ion · 11 copies · chains A, B, D, E
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, D, E
- GOL · Glycerol · additive · 8 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 676 | 0.67 | 0.76 | 55 | GOL |
| 2 | 423 | 0.64 | 0.78 | 42 | GOL |
| 3 | 256 | 0.56 | 0.77 | 35 | empty |
| 4 | 147 | 0.52 | 0.80 | 31 | SO4, GOL |
| 5 | 138 | 0.52 | 0.80 | 29 | GOL |
Interfaces
5 interfaces between chains.
- A–B · 1226 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1214 Ų buried · 22 hydrogen bonds · protein-protein
- D–F · 824 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 817 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 744 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6H6D · Crystal structures of the murine class I major histocompatibility complex H-2Db in… · the same entry in another collection · chain F against F, 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 0.99
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 P03255
- Elsewhere: RCSB PDB 6H6D · PDBe 6H6D · UniProt P01899 · UniProt P01887 · UniProt P03255
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.