MolNFT v1 · #79728 · protein
Crystal structure of the murine class I major histocompatibility complex H-2DB in complex with the lcmv-derived GP33 altered peptide ligand (A2G,V3P,Y4A)
3TBV · H-2 class I histocompatibility antigen, D-B alpha chain: “Crystal structure of the murine class I major histocompatibility complex H-2DB in complex with the…”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.71).…
- PDB
- 3TBV
- Type
- protein
- Length
- 1,536 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
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 276 | 23% helix, 39% strand | P01899 |
| B, D, F, H | Beta-2-microglobulin | protein | 99 | 0% helix, 52% strand | P01887 |
| I, J, K, L | Glycoprotein G1 | protein | 9 | 0% helix, 0% strand | P07399 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, C, D, E, F
- GOL · Glycerol · additive · 7 copies · chains A, B, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 827 | 0.71 | 0.76 | 65 | GOL |
| 2 | 852 | 0.70 | 0.76 | 69 | GOL |
| 3 | 896 | 0.70 | 0.75 | 74 | SO4 |
| 4 | 783 | 0.69 | 0.76 | 72 | GOL |
| 5 | 171 | 0.49 | 0.77 | 35 | empty |
Interfaces
13 interfaces between chains.
- G–H · 1338 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1314 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1304 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 1300 Ų buried · 21 hydrogen bonds · protein-protein
- G–L · 877 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 3TBV · CRYSTAL STRUCTURE OF THE MURINE CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX H-2DB IN COMPLEX… · the same entry in another collection · chain L against L, 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 3TBV · PDBe 3TBV · UniProt P01899 · UniProt P01887 · UniProt P07399
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