Research workbench
Crystal structure of H2-kb in complex with a ova mutant peptide
Analyse Crystal structure of H2-kb in complex with a ova mutant peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JI2
- Type
- protein
- Length
- 768 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; Ova mutant…
- UniProt
- P01901, P01887
- Pockets
- 13 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 20% 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 | 98 | 0% helix, 50% strand | P01887 |
| C, F | Ova mutant peptide | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 8 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 703 | 0.65 | 0.74 | 56 | GOL |
| 2 | 487 | 0.61 | 0.75 | 42 | empty |
| 3 | 184 | 0.49 | 0.77 | 34 | empty |
| 4 | 155 | 0.48 | 0.77 | 34 | empty |
| 5 | 137 | 0.47 | 0.78 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1155 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1110 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 877 Ų buried · 19 hydrogen bonds · protein-protein
- D–F · 865 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 642 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 7JI2 · Crystal Structure of H2-Kb in complex with a OVA mutant peptide · 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 D 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
- Elsewhere: RCSB PDB 7JI2 · PDBe 7JI2 · UniProt P01901 · UniProt P01887
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