Research workbench
Structure of 2Q1-Fab, an antibody selective for IDH2R140Q-HLA-B*07:02
Analyse Structure of 2Q1-Fab, an antibody selective for IDH2R140Q-HLA-B*07:02 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KGU
- Type
- protein
- Length
- 1,690 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain, Fab fragment, IgG; Heavy chain, Fab, IgG, Fab
- Ligands
- GLY, K, SO4, CL
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 7 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Light chain, Fab fragment, IgG | protein | 212 | 7% helix, 51% strand | — |
| B | Heavy chain, Fab, IgG, Fab | protein | 212 | 7% helix, 54% strand | — |
| D | Heavy chain, Fab, IgG, Fab | protein | 212 | 8% helix, 53% strand | — |
| E | Light chain, Fab fragment, IgG | protein | 210 | 4% helix, 51% strand | — |
| F | Heavy chain, Fab, IgG, Fab | protein | 210 | 9% helix, 52% strand | — |
| H | Heavy chain, Fab, IgG, Fab | protein | 211 | 10% helix, 54% strand | — |
| L | Light chain, Fab fragment, IgG | protein | 211 | 6% helix, 51% strand | — |
Ligands and binding sites
- GLY · Glycine · ligand · chains L
- K · Potassium ion · metal · chains H
- SO4 · Sulfate ion · ion · 33 copies · chains A, B, D, F, H, C, L
- CL · Chloride ion · ion · 2 copies · chains F, H, L
- PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains A, C, D, F, H, L
- PG4 · Tetraethylene glycol · additive · 2 copies · chains B, H
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 150 | 0.74 | 0.92 | 21 | empty |
| 2 | 553 | 0.68 | 0.77 | 38 | CL |
| 3 | 501 | 0.64 | 0.76 | 37 | SO4 |
| 4 | 588 | 0.62 | 0.74 | 53 | SO4 |
| 5 | 495 | 0.60 | 0.74 | 61 | empty |
Interfaces
10 interfaces between chains.
- C–D · 1723 Ų buried · 13 hydrogen bonds · protein-protein
- H–L · 1720 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1709 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1701 Ų buried · 13 hydrogen bonds · protein-protein
- B–H · 736 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 7KGU · Structure of 2Q1-Fab, an antibody selective for IDH2R140Q-HLA-B*07:02 · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 7KGU · PDBe 7KGU
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