Research workbench
Murine CD8AA ectodomain fragment in complex with H-2KB/VSV8
Analyse Murine CD8AA ectodomain fragment in complex with H-2KB/VSV8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BQH
- Type
- protein
- Length
- 1,256 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (H-2 class I histocompatibility antigen); Protein (beta-2-microglobulin )…
- UniProt
- P01901, P01887, P01731
- Ligands
- NAG
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 11% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Protein (H-2 class I histocompatibility antigen) | protein | 274 | 27% helix, 40% strand | P01901 |
| B, E | Protein (beta-2-microglobulin ) | protein | 99 | 0% helix, 47% strand | P01887 |
| C, F | Protein (VSV8) | protein | 8 | 0% helix, 0% strand | — |
| G | Protein (CD8A or LYT2 or lyt-2) | protein | 122 | 2% helix, 43% strand | P01731 |
| H, K | Protein (CD8A or LYT2 or lyt-2) | protein | 125 | 2% helix, 50% strand | P01731 |
| I | Protein (CD8A or LYT2 or lyt-2) | protein | 122 | 2% helix, 51% strand | P01731 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains G, H, I, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1034 | 0.81 | 0.83 | 85 | empty |
| 2 | 937 | 0.80 | 0.82 | 86 | empty |
| 3 | 403 | 0.62 | 0.77 | 53 | empty |
| 4 | 322 | 0.59 | 0.77 | 30 | empty |
| 5 | 331 | 0.59 | 0.77 | 40 | empty |
Interfaces
12 interfaces between chains.
- A–B · 1350 Ų buried · 28 hydrogen bonds · protein-protein
- D–E · 1327 Ų buried · 20 hydrogen bonds · protein-protein
- G–H · 1175 Ų buried · 7 hydrogen bonds · protein-protein
- I–K · 1072 Ų buried · 5 hydrogen bonds · protein-protein
- D–F · 900 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 1BQH · Murine CD8AA ectodomain fragment in complex with H-2KB/VSV8 · the same entry in another collection · chain K against K, 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 0.98
- P01901 · AlphaFold monomer V2.0 prediction for H-2 class I histocompatibility antigen, K-B alpha… · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P01901
- Every structure of UniProt P01887
- Every structure of UniProt P01731
- Elsewhere: RCSB PDB 1BQH · PDBe 1BQH · UniProt P01901 · UniProt P01887 · UniProt P01731
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