5YY4: ScFv antibody 4B08 with sulfated epitope peptide

Crystal structure of the scFv antibody 4B08 with sulfated epitope peptide. Determined by X-ray diffraction at 1.59 Å resolution. Released 18 Jul 2018.

Method: X-ray diffraction
Resolution: 1.59 Å
Organisms: Mus musculus, Homo sapiens
Chains: 2
Atoms: 2,250
Mol. weight: 28.39 kDa
Released: 18 Jul 2018

Explore 5YY4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5YY4 contains 8 α-helices and 24 β-strands across 1 chain. 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	141-143	3
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	207-212	6	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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
scFv 4B08	A	protein	252	Mus musculus
C-C chemokine receptor type 5	B	protein	9	Homo sapiens	P51681 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5YY4_1 scFv 4B08 (chains A)
EVQLQQSGAELVRPGTSVKMSCKAAGYTFTKYWIGWVKQRPGHGLEWIGDIHPGSFYSNY
NEKFKGKATLTADTSSSTAYMQLSSLTSEDSAIYYCARDYYTNYGDWGQGTSVTVSSAGG
GGSGGGGSGGGGSGGGGSDIVMTQAAPSVSVTPGESVSISCRSSKSLLHRNGNTYLFWFL
QRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLRISRVEAEDVGVYYCMQHLEYPYT
FGSGTKLELKVR

Sequence of entity 2 (B), FASTA

>5YY4_2 C-C chemokine receptor type 5 (chains B)
DINYYTSEP

Primary citation

Tyrosine Sulfation Restricts the Conformational Ensemble of a Flexible Peptide, Strengthening the Binding Affinity for an Antibody. Miyanabe, K., Yamashita, T., Abe, Y. et al. Biochemistry (2018) 57:4177-4185. DOI 10.1021/acs.biochem.8b00592 · PubMed

Other PDB entries of the same protein (UniProt P51681 (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)
9J8A 1.75 Å, Structure of antibody BA8 in complex with sulfated peptide from CCR5
5YD5 1.96 Å, Crystal structure of the scFv antibody 4B08 with epitope peptide (mutation N3A)
5UIW 2.2 Å, Crystal Structure of CC Chemokine Receptor 5 (CCR5) in complex with high potency HIV…
7F1T 2.6 Å, Crystal structure of the human chemokine receptor CCR5 in complex with MIP-1a
4MBS 2.71 Å, Crystal Structure of the CCR5 Chemokine Receptor
6AKX 2.8 Å, The Crystal structure of Human Chemokine Receptor CCR5 in complex with compound 21
6AKY 2.8 Å, The Crystal structure of Human Chemokine Receptor CCR5 in complex with compound 34
7F1S 2.8 Å, Cryo-EM structure of the apo chemokine receptor CCR5 in complex with Gi
7F1Q 2.9 Å, Cryo-EM structure of the chemokine receptor CCR5 in complex with MIP-1a and Gi
7F1R 3.0 Å, Cryo-EM structure of the chemokine receptor CCR5 in complex with RANTES and Gi

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