Research workbench
Local and transmitted conformational changes on complexation of an anti-sweetener Fab
Analyse Local and transmitted conformational changes on complexation of an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CGR
- Type
- protein
- Length
- 433 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG2B-kappa NC6.8 Fab (light chain); IGG2B-kappa NC6.8 Fab (heavy chain)
- Ligands
- GAS
- Pockets
- 6 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | IGG2B-kappa NC6.8 Fab (light chain) | protein | 219 | 6% helix, 49% strand | — |
| H | IGG2B-kappa NC6.8 Fab (heavy chain) | protein | 214 | 4% helix, 55% strand | — |
Ligands and binding sites
- GAS · N-(P-cyanophenyl)-N'-diphenylmethyl-guanidine-acetic acid · ligand · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.46 | 0.83 | 20 | GAS |
| 2 | 78 | 0.38 | 0.78 | 16 | empty |
| 3 | 90 | 0.33 | 0.74 | 23 | empty |
| 4 | 77 | 0.32 | 0.74 | 18 | empty |
| 5 | 63 | 0.32 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- L–H · 1815 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 2CGR · Local and transmitted conformational changes on complexation of an anti-sweetener Fab · the same entry in another collection · chain L against L, 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 2CGR · PDBe 2CGR
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