1P4B: Single Chain Fv Fragment

Three-Dimensional Structure Of a Single Chain Fv Fragment Complexed With The peptide GCN4(7P-14P). Determined by X-ray diffraction at 2.35 Å resolution. Released 4 May 2004.

Method: X-ray diffraction
Resolution: 2.35 Å
Organism: Mus musculus
Chains: 3
Atoms: 1,875
Mol. weight: 28.19 kDa
Released: 4 May 2004

Explore 1P4B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1P4B contains 6 α-helices and 22 β-strands across 3 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: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	3-11	8	4
β-strand	19-26	8	4
β-strand	41-46	6	5
β-strand	52-58	7	5
β-strand	68-70	3	5
α-helix	75-77	3
β-strand	78-83	6	4
β-strand	88-93	6	4
α-helix	98-100	3
β-strand	102-107	6	5
β-strand	139	1	5
β-strand	143-145	3	5

Chain L: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	1
β-strand	10-13	4	2
β-strand	18-23	6	3
β-strand	24-25	2	1
α-helix	33-39	3
β-strand	42-47	6	2
α-helix	48-50	3
β-strand	51-57	7	2
β-strand	69-70	2	2
β-strand	78-83	6	3
β-strand	88-94	7	3
α-helix	98-100	3
β-strand	102-109	8	2
β-strand	137-139	3	2
β-strand	143-147	5	2

Chain P: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-10	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antibody Variable light chain	L	protein	135	Mus musculus	P01723 (AlphaFold model)
Antibody Variable heavy chain	H	protein	124	Mus musculus	P01820 (AlphaFold model)
GCN4(7P-14P) peptide	P	protein	12

Sequence of entity 1 (L), FASTA

>1P4B_1 Antibody Variable light chain (chains L)
MADYADAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYASWVQEKPDHLFTGLIGGTNN
RAPGVPARFSGSLIGDKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVLGGGGGS
GGGGSGGGGSGGGGS

Sequence of entity 2 (H), FASTA

>1P4B_2 Antibody Variable heavy chain (chains H)
DVQLQQSGPGLVAPSQSLSITCTVSGFSLTDYGVNWVRQSPGKGLEWLGVIWGDGITDYN
SALKSRLSVTKDNSKSQVFLKMNSLQSGDSARYYCVTGLFDYWGQGTTLTVSSASGADHH
HHHH

Sequence of entity 3 (P), FASTA

>1P4B_3 GCN4(7P-14P) peptide (chains P)
AHLENEVARLKK

Primary citation

Directed in Vitro Evolution and Crystallographic Analysis of a Peptide-binding Single Chain Antibody Fragment (scFv) with Low Picomolar Affinity. Zahnd, C., Spinelli, S., Amstutz, P. et al. J Biol Chem (2004) 279:18870-18877. DOI 10.1074/jbc.M309169200 · PubMed

Other PDB entries of the same protein (UniProt P01723 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1Q0X 1.6 Å, Anti-morphine Antibody 9B1 Unliganded Form
1SM3 1.95 Å, Crystal structure of the tumor specific antibody SM3 complex with its peptide epitope
3CFJ 2.6 Å, Crystal structure of catalytic elimination antibody 34E4, orthorhombic crystal form
3CFK 2.6 Å, Crystal structure of catalytic elimination antibody 34E4, triclinic crystal form
1P4I 2.8 Å, Crystal Structure of scFv against peptide GCN4

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