Research workbench
Crystal structure of H-2KB in complex with jhmv epitope S598
Analyse Crystal structure of H-2KB in complex with jhmv epitope S598 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZSV
- Type
- protein
- Length
- 765 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class I histocompatibility antigen, K-B alpha chain; Beta-2-microglobulin; 8-mer…
- UniProt
- P01901, P01887
- Ligands
- CYS
- Pockets
- 12 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, K-B alpha chain | protein | 274 | 27% helix, 40% strand | P01901 |
| B, D | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P01887 |
| C | H-2 class I histocompatibility antigen, K-B alpha chain | protein | 277 | 25% helix, 39% strand | P01901 |
| E, F | 8-mer peptide from spike glycoprotein | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 542 | 0.61 | 0.74 | 57 | GOL |
| 2 | 472 | 0.59 | 0.74 | 46 | GOL |
| 3 | 161 | 0.50 | 0.78 | 28 | empty |
| 4 | 136 | 0.50 | 0.79 | 21 | empty |
| 5 | 124 | 0.44 | 0.77 | 24 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1179 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1176 Ų buried · 20 hydrogen bonds · protein-protein
- C–F · 846 Ų buried · 21 hydrogen bonds · protein-protein
- A–E · 844 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 639 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 modified, 1 covalent (disulfide, nonstandard, covalent ligand).
Compared structures
- 2ZSV · Crystal structure of H-2Kb in complex with JHMV epitope S598 · 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
- P01901 · AlphaFold monomer V2.0 prediction for H-2 class I histocompatibility antigen, K-B alpha… · a predicted model of the same protein · chain C against A, TM-score 0.93
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
- Elsewhere: RCSB PDB 2ZSV · PDBe 2ZSV · UniProt P01901 · UniProt P01887
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