Research workbench
Crystal structure of HLA-B*07:02 with wild-type IDH2 peptide
Analyse Crystal structure of HLA-B*07:02 with wild-type IDH2 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UJ8
- Type
- protein
- Length
- 772 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
- SO4
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | HLA class I histocompatibility antigen, B-7 alpha chain | protein | 275 | 28% helix, 40% 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 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, D, E
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B, D, E
- 1PE · Pentaethylene glycol · additive · chains A, B
- PGE · Triethylene glycol · additive · chains A, B
- PG4 · Tetraethylene glycol · additive · chains D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 927 | 0.83 | 0.85 | 106 | PEG, 1PE |
| 2 | 260 | 0.70 | 0.85 | 35 | PG4, PEG, SO4 |
| 3 | 99 | 0.47 | 0.80 | 25 | empty |
| 4 | 97 | 0.45 | 0.79 | 18 | empty |
| 5 | 52 | 0.44 | 0.84 | 17 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1475 Ų buried · 24 hydrogen bonds · protein-protein
- D–E · 1453 Ų buried · 21 hydrogen bonds · protein-protein
- D–F · 924 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 913 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 540 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6UJ8 · Crystal structure of HLA-B*07:02 with wild-type 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 0.98
- P48735 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NADP], mitochondrial… · a predicted model of the same protein · chain C against A, TM-score 0.35
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 6UJ8 · PDBe 6UJ8 · UniProt P01889 · UniProt P61769 · UniProt P48735
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