Research workbench
Antibody Fab fragment targeting gi protein heterotrimer
Analyse Antibody Fab fragment targeting gi protein heterotrimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QNK
- Type
- protein
- Length
- 876 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab light chain; Fab heavy chain
- Ligands
- MLT
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Fab light chain | protein | 217 | 6% helix, 49% strand | — |
| B, D | Fab heavy chain | protein | 221 | 5% helix, 52% strand | — |
Ligands and binding sites
- MLT · D-malate · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, B, C, D
- PG4 · Tetraethylene glycol · additive · 3 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 520 | 0.73 | 0.81 | 77 | empty |
| 2 | 299 | 0.61 | 0.79 | 54 | MLT |
| 3 | 157 | 0.49 | 0.77 | 29 | EDO |
| 4 | 139 | 0.48 | 0.78 | 33 | empty |
| 5 | 101 | 0.45 | 0.79 | 21 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1806 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1805 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 581 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 476 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 covalent (disulfide, additive adduct, covalent ligand).
Compared structures
- 6QNK · Antibody FAB fragment targeting Gi protein heterotrimer · 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 6QNK · PDBe 6QNK
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