1N4X: ScFv 1696 at acidic pH

Structure of scFv 1696 at acidic pH. Determined by X-ray diffraction at 1.7 Å resolution. Released 10 Jun 2003.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Mus musculus
Chains: 4
Atoms: 4,188
Mol. weight: 52.08 kDa
Released: 10 Jun 2003

Explore 1N4X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1N4X contains 15 α-helices and 44 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain H: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	303-306	4	3
α-helix	307-309	3
β-strand	310-312	3	4
β-strand	318-325	8	3
α-helix	329-331	3
β-strand	334-339	6	4
β-strand	345-352	8	4
β-strand	357-360	4	4
β-strand	368-373	6	3
α-helix	374-376	3
β-strand	378-383	6	3
α-helix	388-390	3
β-strand	392-399	8	4
β-strand	407-410	4	4
β-strand	414-418	5	4

Chain I: 5 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	303-306	4	7
α-helix	307-309	3
β-strand	310-312	3	8
β-strand	318-325	8	7
α-helix	329-331	3
β-strand	334-339	6	8
β-strand	345-351	7	8
β-strand	358-360	3	8
α-helix	362-364	3
β-strand	368-373	6	7
α-helix	374-376	3
β-strand	378-383	6	7
α-helix	388-390	3
β-strand	392-399	8	8
β-strand	407-410	4	8
β-strand	414-418	5	8

Chain L: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	38-43	6	2
β-strand	50-54	5	2
β-strand	58-59	2	2
α-helix	60	1
β-strand	67-71	5	1
β-strand	75-80	6	1
α-helix	85-87	3
β-strand	89-95	7	2
α-helix	101	1
β-strand	102-103	2	2
β-strand	107-111	5	2

Chain M: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	5
β-strand	10-13	4	6
β-strand	19-25	7	5
β-strand	38-43	6	6
β-strand	50-54	5	6
β-strand	58-59	2	6
α-helix	60	1
β-strand	67-72	6	5
β-strand	75-80	6	5
α-helix	85-87	3
β-strand	89-95	7	6
α-helix	101	1
β-strand	102-103	2	6
β-strand	107-111	5	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
immunoglobulin kappa chain variable region	L, M	protein	113	Mus musculus	P01631 (AlphaFold model)
immunoglobulin heavy chain variable region	H, I	protein	120	Mus musculus	Q921A6 (AlphaFold model)

Sequence of entity 1 (L, M), FASTA

>1N4X_1 immunoglobulin kappa chain variable region (chains L, M)
MDILMTQTPLYLPVSLGDQASISCRSSQTIVHNNGNTYLEWYLQKPGQSPQLLIYKVSNR
FSGVPDRFSGSGSGTDFTLKISRVEAEDLGIYYCFQGSHFPPTFGGGTKLEIA

Sequence of entity 2 (H, I), FASTA

>1N4X_2 immunoglobulin heavy chain variable region (chains H, I)
EVQLQQSGPELKKPGETVKISCKATNYAFTDYSMHWVKQAPGGDLKYVGWINTETDEPTF
ADDFKGRFAFSLDTSTSTAFLQINNLKNEDTATYFCVRDRHDYGEIFTYWGQGTTVTVSA

Primary citation

Structure of a single-chain Fv fragment of an antibody that inhibits the HIV-1 and HIV-2 proteases. Lescar, J., Brynda, J., Fabry, M. et al. Acta Crystallogr D Biol Crystallogr (2003) 59:955-957. DOI 10.1107/S0907444903003597 · PubMed

Other PDB entries of the same protein (UniProt P01631 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1DLF 1.45 Å, High resolution crystal structure of the fv fragment from an anti-dansyl switch variant…
2DLF 1.55 Å, High resolution crystal structure of the fv fragment from an anti-dansyl switch variant…
1WZ1 1.85 Å, Crystal structure of the Fv fragment complexed with dansyl-lysine
1SVZ 1.89 Å, Crystal structure of the single-chain Fv fragment 1696 in complex with the epitope…
2IPT 2.0 Å, PFA1 Fab Fragment
2IQA 2.0 Å, PFA2 FAB fragment, monoclinic apo form
2HKF 2.01 Å, Crystal structure of the Complex Fab M75- Peptide
2O5X 2.05 Å, Crystal structure of 1E9 LeuH47Trp/ArgH100Trp, an engineered Diels-Alderase Fab with nM…
1BFV 2.1 Å, Monoclonal antibody fragment FV4155 from E. Coli
1CFV 2.1 Å, Monoclonal antibody fragment FV4155 from E. Coli
2HKH 2.1 Å, Crystal structure of the Fab M75
2O5Z 2.4 Å, Crystal structure of the 1E9 LeuH47Trp/ArgH100Trp Fab 5-beta-androstane-3,17-dione complex

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