Research workbench
Crystal structure of HLA-B*07:02 with R140Q mutant IDH2 peptide
Analyse Crystal structure of HLA-B*07:02 with R140Q mutant IDH2 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UJ7
- Type
- protein
- Length
- 780 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, B-7 alpha chain; Beta-2-microglobulin; Isocitrate…
- EC
- 1.1.1.42
- UniProt
- P01889, P61769, P48735
- Ligands
- NA, K, SO4
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, B-7 alpha chain | protein | 280 | 28% helix, 39% strand | P01889 |
| B, E | Beta-2-microglobulin | protein | 101 | 0% helix, 49% strand | P61769 |
| C, F | Isocitrate dehydrogenase [NADP], mitochondrial (EC 1.1.1.42) | protein | 10 | 0% helix, 0% strand | P48735 |
| D | HLA class I histocompatibility antigen, B-7 alpha chain | protein | 278 | 27% helix, 39% strand | P01889 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, B, D
- K · Potassium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 517 | 0.80 | 0.87 | 84 | NA |
| 2 | 249 | 0.73 | 0.88 | 35 | empty |
| 3 | 178 | 0.69 | 0.87 | 26 | empty |
| 4 | 63 | 0.46 | 0.84 | 16 | empty |
| 5 | 92 | 0.45 | 0.80 | 25 | empty |
Interfaces
8 interfaces between chains.
- D–E · 1439 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1424 Ų buried · 21 hydrogen bonds · protein-protein
- D–F · 876 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 873 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 585 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6UJ7 · Crystal structure of HLA-B*07:02 with R140Q mutant IDH2 peptide · the same entry in another collection · chain F against F, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P01889 · AlphaFold monomer V2.0 prediction for HLA class I histocompatibility antigen, B alpha… · a predicted model of the same protein · chain A against A, TM-score 0.96
- P48735 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NADP], mitochondrial… · a predicted model of the same protein · chain C against A, TM-score 0.38
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 P01889
- Every structure of UniProt P61769
- Every structure of UniProt P48735
- Elsewhere: RCSB PDB 6UJ7 · PDBe 6UJ7 · UniProt P01889 · UniProt P61769 · UniProt P48735
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