MolNFT v1 · #166216 · protein
Crystal structure of HLA-B*07:02 with R140Q mutant IDH2 peptide in complex with Fab
6UJ9 · HLA class I histocompatibility antigen, B-7 alpha chain: “Crystal structure of HLA-B*07:02 with R140Q mutant IDH2 peptide in complex with Fab”. X-ray diffraction, 1 ligand (SO4), 7 pockets (best druggability 0.69). MolNFT v1 #166216…
- PDB
- 6UJ9
- Type
- protein
- Length
- 818 residues
- Chains
- 5
- 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
- 7 · best druggability 0.69
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, B-7 alpha chain | protein | 277 | 25% helix, 39% strand | P01889 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Isocitrate dehydrogenase [NADP], mitochondrial (EC 1.1.1.42) | protein | 10 | 0% helix, 0% strand | P48735 |
| L | Fab light chain | protein | 213 | 5% helix, 51% strand | — |
| H | Fab heavy chain | protein | 218 | 3% helix, 52% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, H, B
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B, L
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 555 | 0.69 | 0.79 | 53 | NHE, PEG |
| 2 | 526 | 0.60 | 0.74 | 60 | empty |
| 3 | 136 | 0.45 | 0.77 | 26 | SO4 |
| 4 | 87 | 0.39 | 0.77 | 18 | SO4 |
| 5 | 60 | 0.36 | 0.78 | 15 | empty |
Interfaces
7 interfaces between chains.
- L–H · 1989 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1372 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 897 Ų buried · 21 hydrogen bonds · protein-protein
- A–H · 734 Ų buried · 9 hydrogen bonds · protein-protein
- A–L · 379 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 6UJ9 · Crystal structure of HLA-B*07:02 with R140Q mutant IDH2 peptide in complex with Fab · the same entry in another collection · chain H against H, 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 0.97
- P48735 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NADP], mitochondrial… · a predicted model of the same protein · chain C against A, TM-score 0.47
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 6UJ9 · PDBe 6UJ9 · UniProt P01889 · UniProt P61769 · UniProt P48735
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