5YD5: ScFv antibody 4B08 with epitope peptide

Crystal structure of the scFv antibody 4B08 with epitope peptide (mutation N3A). Determined by X-ray diffraction at 1.96 Å resolution. Released 6 Jun 2018.

Method: X-ray diffraction
Resolution: 1.96 Å
Organisms: Mus musculus, Homo sapiens
Chains: 4
Atoms: 4,280
Mol. weight: 56.38 kDa
Released: 6 Jun 2018

Explore 5YD5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5YD5 contains 15 α-helices and 50 β-strands across 2 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 A: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	1
α-helix	9-11	3
β-strand	12-14	3	2
β-strand	20-27	8	1
β-strand	36-41	6	2
β-strand	47-53	7	2
β-strand	60-62	3	2
α-helix	64-66	3
β-strand	70-75	6	1
β-strand	80-85	6	1
α-helix	90-92	3
β-strand	94-102	9	2
β-strand	105-109	5	2
β-strand	113-117	5	2
β-strand	122	1	2
α-helix	140-143	4
β-strand	144-145	2	3
β-strand	150-153	4	4
β-strand	159-165	7	3
β-strand	170	1	5
β-strand	176	1	5
β-strand	178-183	6	4
β-strand	190-194	5	4
β-strand	198-199	2	4
α-helix	200	1
β-strand	207-211	5	3
β-strand	215-220	6	3
α-helix	225-227	3
β-strand	229-235	7	4
α-helix	241	1
β-strand	242-243	2	4
β-strand	247-251	5	4

Chain C: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	6
α-helix	9-11	3
β-strand	12-14	3	7
β-strand	20-27	8	6
α-helix	31-33	3
β-strand	36-41	6	7
β-strand	47-53	7	7
β-strand	60-62	3	7
α-helix	64-66	3
β-strand	70-75	6	6
β-strand	80-85	6	6
α-helix	90-92	3
β-strand	94-102	9	7
β-strand	105-109	5	7
β-strand	113-117	5	7
β-strand	122	1	7
α-helix	140-143	4
β-strand	144-145	2	8
β-strand	150-153	4	9
β-strand	159-165	7	8
β-strand	170	1	10
β-strand	176	1	10
β-strand	178-183	6	9
β-strand	190-194	5	9
β-strand	198-199	2	9
α-helix	200	1
β-strand	207-211	5	8
β-strand	215-220	6	8
α-helix	225-227	3
β-strand	229-235	7	9
α-helix	241	1
β-strand	242-243	2	9
β-strand	247-251	5	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
scFv 4B08	A, C	protein	251	Mus musculus	P01630 (AlphaFold model)
Peptide epitope (mutation N3A)	B, D	protein	9	Homo sapiens	P51681 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5YD5_1 scFv 4B08 (chains A, C)
EVQLQQSGAELVRPGTSVKMSCKAAGYTFTKYWIGWVKQRPGHGLEWIGDIHPGSFYSNY
NEKFKGKATLTADTSSSTAYMQLSSLTSEDSAIYYCARDYYTNYGDWGQGTSVTVSSAGG
GGSGGGGSGGGGSGGGGSDIVMTQAAPSVSVTPGESVSISCRSSKSLLHRNGNTYLFWFL
QRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLRISRVEAEDVGVYYCMQHLEYPYT
FGSGTKLELKV

Sequence of entity 2 (B, D), FASTA

>5YD5_2 Peptide epitope (mutation N3A) (chains B, D)
DIAYYTSEP

Primary citation

Intramolecular H-bonds govern the recognition of a flexible peptide by an antibody. Miyanabe, K., Akiba, H., Kuroda, D. et al. J Biochem (2018) 164:65-76. DOI 10.1093/jb/mvy032 · PubMed

Other PDB entries of the same protein (UniProt P01630 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5YD3 1.35 Å, Crystal structure of the scFv antibody 4B08 with epitope peptide
5YD4 1.35 Å, Crystal structure of the scFv antibody 4B08 with epitope peptide (mutation T6A)

Browse structure collections

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