MolNFT v1 · #79726 · protein
Crystal structure of the murine class I major histocompatibility complex H-2DB in complex the with lcmv-derived GP33 altered peptide ligand (V3P,Y4A)
3TBS · H-2 class I histocompatibility antigen, D-B alpha chain: “Crystal structure of the murine class I major histocompatibility complex H-2DB in complex the with…”. X-ray diffraction, 1 ligand (SO4), 11 pockets (best druggability 0.66).…
- PDB
- 3TBS
- Type
- protein
- Length
- 759 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
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 272 | 26% helix, 40% strand | P01899 |
| B, E | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P01887 |
| C, F | Glycoprotein G1 | protein | 9 | 0% helix, 0% strand | P07399 |
| D | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 271 | 25% helix, 40% strand | P01899 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 539 | 0.66 | 0.77 | 51 | empty |
| 2 | 433 | 0.65 | 0.78 | 42 | empty |
| 3 | 166 | 0.52 | 0.79 | 32 | empty |
| 4 | 170 | 0.52 | 0.79 | 38 | empty |
| 5 | 90 | 0.40 | 0.78 | 17 | empty |
Interfaces
5 interfaces between chains.
- D–E · 1306 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1276 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 884 Ų buried · 26 hydrogen bonds · protein-protein
- D–F · 876 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 752 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3TBS · CRYSTAL STRUCTURE OF THE MURINE CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX H-2DB IN COMPLEX… · 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 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 P07399
- Elsewhere: RCSB PDB 3TBS · PDBe 3TBS · UniProt P01899 · UniProt P01887 · UniProt P07399
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