Research workbench
Structure of scfv 1696 at acidic pH
Analyse Structure of scfv 1696 at acidic pH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1N4X
- Type
- protein
- Length
- 465 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin kappa chain variable region; Immunoglobulin heavy chain variable region
- UniProt
- Q99M37, Q921A6
- Ligands
- CL
- Pockets
- 7 · best druggability 0.39
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, M | Immunoglobulin kappa chain variable region | protein | 113 | 3% helix, 47% strand | Q99M37 |
| H | Immunoglobulin heavy chain variable region | protein | 120 | 8% helix, 52% strand | Q921A6 |
| I | Immunoglobulin heavy chain variable region | protein | 119 | 10% helix, 50% strand | Q921A6 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.39 | 0.78 | 24 | empty |
| 2 | 50 | 0.39 | 0.81 | 21 | empty |
| 3 | 132 | 0.36 | 0.72 | 26 | empty |
| 4 | 98 | 0.36 | 0.74 | 22 | empty |
| 5 | 63 | 0.32 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- M–I · 943 Ų buried · 11 hydrogen bonds · protein-protein
- L–H · 897 Ų buried · 9 hydrogen bonds · protein-protein
- L–I · 77 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1N4X · Structure of scFv 1696 at acidic pH · 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
- Every structure of UniProt Q99M37
- Every structure of UniProt Q921A6
- Elsewhere: RCSB PDB 1N4X · PDBe 1N4X · UniProt Q99M37 · UniProt Q921A6
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