Research workbench
The three-dimensional structure of an anti-sweetener Fab, NC10.14, shows the extent of structural diversity in antigen recognition by immunoglobulins
Analyse The three-dimensional structure of an anti-sweetener Fab, NC10.14, shows the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ETZ
- Type
- protein
- Length
- 886 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab NC10.14 - light chain; Fab NC10.14 - heavy chain
- Ligands
- GAS
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A | Fab NC10.14 - light chain | protein | 215 | 7% helix, 54% strand | — |
| H, B | Fab NC10.14 - heavy chain | protein | 228 | 3% helix, 51% strand | — |
Ligands and binding sites
- GAS · N-(P-cyanophenyl)-N'-diphenylmethyl-guanidine-acetic acid · ligand · 2 copies · chains L, H, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 875 | 0.76 | 0.79 | 94 | empty |
| 2 | 566 | 0.71 | 0.80 | 74 | empty |
| 3 | 688 | 0.70 | 0.78 | 62 | empty |
| 4 | 379 | 0.60 | 0.77 | 49 | empty |
| 5 | 103 | 0.45 | 0.79 | 18 | empty |
Interfaces
5 interfaces between chains.
- L–H · 2094 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 2016 Ų buried · 11 hydrogen bonds · protein-protein
- L–A · 532 Ų buried · 4 hydrogen bonds · protein-protein
- H–A · 350 Ų buried · 7 hydrogen bonds · protein-protein
- L–B · 338 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 1ETZ · The three-dimensional structure of an anti-sweetener Fab, NC10.14, shows the extent of… · 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 1ETZ · PDBe 1ETZ
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