Research workbench
Crystal structure of H2-kb in complex with a mutant of the chicken ovalbumin epitope ova-E1
Analyse Crystal structure of H2-kb in complex with a mutant of the chicken ovalbumin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PAB
- Type
- protein
- Length
- 771 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
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, K-B alpha chain | protein | 279 | 23% helix, 38% strand | P01901 |
| B, E | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P01887 |
| C, F | Ovalbumin epitope, eiinfekl | protein | 8 | 0% helix, 0% strand | P01012 |
| D | H-2 class I histocompatibility antigen, K-B alpha chain | protein | 278 | 27% helix, 39% strand | P01901 |
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 803 | 0.68 | 0.75 | 75 | empty |
| 2 | 684 | 0.66 | 0.75 | 58 | empty |
| 3 | 148 | 0.50 | 0.79 | 20 | empty |
| 4 | 119 | 0.47 | 0.79 | 27 | empty |
| 5 | 137 | 0.45 | 0.77 | 22 | empty |
Interfaces
5 interfaces between chains.
- D–E · 1209 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1184 Ų buried · 18 hydrogen bonds · protein-protein
- A–F · 925 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 901 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 735 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3PAB · Crystal Structure of H2-Kb in complex with a mutant of the chicken ovalbumin epitope… · the same entry in another collection · chain D against D, TM-score 1.00
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain E 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 0.54
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 3PAB · PDBe 3PAB · UniProt P01901 · UniProt P01887 · UniProt P01012
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