MolNFT v1 · #34608 · protein
High resolution crystal structure of the fv fragment from an anti-dansyl switch variant antibody IGG2A(S) crystallized at pH 6.75
2DLF · Protein (anti-dansyl immunoglobulin IGG2A(S)- kappa (light…: “High resolution crystal structure of the fv fragment from an anti-dansyl switch variant antibody IGG2A(S)…”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best…
- PDB
- 2DLF
- Type
- protein
- Length
- 233 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (anti-dansyl immunoglobulin IGG2A(S)- kappa (light chain)); Protein (anti-dansyl…
- UniProt
- P01631, P01801
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.37
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Protein (anti-dansyl immunoglobulin IGG2A(S)- kappa (light chain)) | protein | 113 | 3% helix, 50% strand | P01631 |
| H | Protein (anti-dansyl immunoglobulin IGG2A(S) (heavy chain)) | protein | 120 | 10% helix, 50% strand | P01801 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.37 | 0.76 | 17 | empty |
| 2 | 76 | 0.31 | 0.73 | 22 | empty |
Interfaces
1 interface between chains.
- L–H · 713 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2DLF · High resolution crystal structure of the fv fragment from an anti-dansyl switch variant… · the same entry in another collection · chain L against L, TM-score 1.00
- P01631 · AlphaFold monomer V2.0 prediction for ig kappa chain V-II region 26-10 (P01631) · a predicted model of the same protein · chain L against A, TM-score 0.98
- P01801 · AlphaFold monomer V2.0 prediction for ig heavy chain V-III region J606 (P01801) · a predicted model of the same protein · chain H against A, TM-score 0.94
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 P01631
- Every structure of UniProt P01801
- Elsewhere: RCSB PDB 2DLF · PDBe 2DLF · UniProt P01631 · UniProt P01801
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