5YD3: ScFv antibody 4B08 with epitope peptide

Crystal structure of the scFv antibody 4B08 with epitope peptide. Determined by X-ray diffraction at 1.35 Å resolution. Released 6 Jun 2018.

Method: X-ray diffraction
Resolution: 1.35 Å
Organisms: Mus musculus, Homo sapiens
Chains: 8
Atoms: 8,826
Mol. weight: 112.45 kDa
Released: 6 Jun 2018

Explore 5YD3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5YD3 contains 29 α-helices and 96 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 A: 8 helices, 24 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
α-helix	31-33	3
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
α-helix	142-143	2
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	189-194	6	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: 7 helices, 24 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
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
α-helix	141-143	3
β-strand	144-145	2	8
β-strand	150-153	4	7
β-strand	159-165	7	8
β-strand	170	1	9
β-strand	176	1	9
β-strand	178-183	6	7
β-strand	190-194	5	7
β-strand	198-199	2	7
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	7
α-helix	241	1
β-strand	242-243	2	7
β-strand	247-251	5	7

Chain E: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	10
β-strand	12-14	3	11
β-strand	20-27	8	10
α-helix	31-33	3
β-strand	36-41	6	11
β-strand	47-54	8	11
β-strand	59-62	4	11
α-helix	64-66	3
β-strand	70-75	6	10
β-strand	80-85	6	10
α-helix	90-92	3
β-strand	94-102	9	11
β-strand	105-109	5	11
β-strand	113-117	5	11
α-helix	141-143	3
β-strand	144-145	2	12
β-strand	150-153	4	13
β-strand	159-165	7	12
β-strand	170	1	14
β-strand	176	1	14
β-strand	178-183	6	13
β-strand	190-194	5	13
β-strand	198-199	2	13
α-helix	200	1
β-strand	207-211	5	12
β-strand	215-220	6	12
α-helix	225-227	3
β-strand	229-235	7	13
α-helix	241	1
β-strand	242-243	2	13
β-strand	247-251	5	13

Chain G: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	15
β-strand	12-14	3	16
β-strand	20-27	8	15
β-strand	36-41	6	16
β-strand	47-53	7	16
β-strand	60-62	3	16
α-helix	64-66	3
β-strand	70-75	6	15
α-helix	76-78	3
β-strand	80-85	6	15
α-helix	90-92	3
β-strand	94-102	9	16
β-strand	105-109	5	16
β-strand	113-117	5	16
α-helix	142-143	2
β-strand	144-145	2	17
β-strand	150-152	3	18
β-strand	159-165	7	17
β-strand	170	1	19
β-strand	176	1	19
β-strand	178-183	6	18
β-strand	190-194	5	18
β-strand	198-199	2	18
α-helix	200	1
β-strand	207-211	5	17
β-strand	215-220	6	17
α-helix	225-227	3
β-strand	229-235	7	18
α-helix	241	1
β-strand	242-243	2	18
β-strand	247-250	4	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
scFv 4B08	A, C, E, G	protein	251	Mus musculus	P01630 (AlphaFold model)
Epitope peptide	B, D, F, H	protein	9	Homo sapiens	P51681 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>5YD3_1 scFv 4B08 (chains A, C, E, G)
EVQLQQSGAELVRPGTSVKMSCKAAGYTFTKYWIGWVKQRPGHGLEWIGDIHPGSFYSNY
NEKFKGKATLTADTSSSTAYMQLSSLTSEDSAIYYCARDYYTNYGDWGQGTSVTVSSAGG
GGSGGGGSGGGGSGGGGSDIVMTQAAPSVSVTPGESVSISCRSSKSLLHRNGNTYLFWFL
QRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLRISRVEAEDVGVYYCMQHLEYPYT
FGSGTKLELKV

Sequence of entity 2 (B, D, F, H), FASTA

>5YD3_2 Epitope peptide (chains B, D, F, H)
DINYYTSEP

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:

5YD4 1.35 Å, Crystal structure of the scFv antibody 4B08 with epitope peptide (mutation T6A)
5YD5 1.96 Å, Crystal structure of the scFv antibody 4B08 with epitope peptide (mutation N3A)

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