Research workbench
Crystal structure of H2-kb in complex with the chicken ovalbumin epitope ova
Analyse Crystal structure of H2-kb in complex with the chicken ovalbumin epitope ova in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P9L
- Type
- protein
- Length
- 770 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; Ovalbumin…
- UniProt
- P01901, P01887, P01012
- Ligands
- CA
- Pockets
- 13 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | H-2 class I histocompatibility antigen, K-B alpha chain | protein | 278 | 27% helix, 39% strand | P01901 |
| B, E | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P01887 |
| C, F | Ovalbumin epitope, siinfekl | protein | 8 | 0% helix, 0% strand | P01012 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 514 | 0.61 | 0.74 | 45 | CA |
| 2 | 448 | 0.58 | 0.74 | 45 | CA |
| 3 | 205 | 0.56 | 0.79 | 29 | empty |
| 4 | 103 | 0.52 | 0.83 | 20 | empty |
| 5 | 196 | 0.52 | 0.78 | 36 | empty |
Interfaces
5 interfaces between chains.
- D–E · 1189 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1122 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 867 Ų buried · 16 hydrogen bonds · protein-protein
- A–F · 865 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 670 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3P9L · Crystal Structure of H2-Kb in complex with the chicken ovalbumin epitope OVA · 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
- P01012 · AlphaFold monomer V2.0 prediction for ovalbumin (P01012) · a predicted model of the same protein · chain C against A, TM-score 0.52
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 P01012
- Elsewhere: RCSB PDB 3P9L · PDBe 3P9L · UniProt P01901 · UniProt P01887 · UniProt P01012
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