9KKU: Helix-loop-helix peptide

Helix-loop-helix peptide (M49) in complex with VEGF-A. Determined by X-ray diffraction at 1.46 Å resolution. Released 11 Dec 2024.

Method: X-ray diffraction
Resolution: 1.46 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 2,357
Mol. weight: 33.28 kDa
Released: 11 Dec 2024

Explore 9KKU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9KKU contains 14 α-helices and 18 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: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	1
α-helix	17-24	8
β-strand	25	1	2
β-strand	27-34	8	3
α-helix	35-38	4
α-helix	40-42	3
β-strand	46-48	3	4
β-strand	51-58	8	3
β-strand	60	1	2
β-strand	66-83	18	4
β-strand	90-106	17	4

Chain B: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	14	1
β-strand	15	1	4
α-helix	16	1
α-helix	17-24	8
β-strand	25	1	5
β-strand	27-34	8	6
α-helix	35-38	4
β-strand	46-48	3	1
β-strand	51-58	8	6
β-strand	60	1	5
β-strand	66-83	18	1
β-strand	90-106	17	1

Chain C: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	2-13	12
β-strand	24	1	7
α-helix	26-29	4
α-helix	30-37	8

Chain D: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	2-13	12
α-helix	22-23	2
β-strand	24	1	7
α-helix	25	1
α-helix	26-41	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vascular endothelial growth factor A, long form	A, B	protein	102	Homo sapiens	P15692 (AlphaFold model)
M49	C, D	protein	43	synthetic construct

Sequence of entity 1 (A, B), FASTA

>9KKU_1 Vascular endothelial growth factor A, long form (chains A, B)
GQNHHEVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLE
CVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPKKD

Sequence of entity 2 (C, D), FASTA

>9KKU_2 M49 (chains C, D)
CAAELAALEAELAALEGPWKGYPIPYGKLQFLIKKLKQLKVAC

Primary citation

Structural Insights into Helix-Loop-Helix Peptides for "Ligand-Targeting" Intracellular Drug Delivery via VEGF Receptor-Mediated Endocytosis. Michigami, M., Kira, R., Kamo, M. et al. Biochem Biophys Res Commun (2024) 741:150980-150980. DOI 10.1016/j.bbrc.2024.150980 · PubMed

Other PDB entries of the same protein (UniProt P15692 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1MKK 1.32 Å, Disulfide deficient mutant of vascular endothelial growth factor A (C61A and C104A)
9JU1 1.45 Å, Helix-loop-helix peptide (VS42-LR3) in complex with VEGF-A
4GLN 1.6 Å, Crystal Structure of Chemically Synthesized Heterochiral {D-Protein Antagonist plus…
4GLS 1.6 Å, Crystal Structure of Chemically Synthesized Heterochiral {D-Protein Antagonist plus…
6ZBR 1.6 Å, VEGF-A 13:107 crystallized with 4C bicyclic peptide
6ZFL 1.6 Å, High resolution structure of VEGF-A 12:107 crystallized in tetragonal form
1FLT 1.7 Å, Vegf in complex with domain 2 of the flt-1 receptor
4KZN 1.71 Å, crystal structure of human VEGF-A receptor binding domain
4QAF 1.8 Å, Crystal structure of an engineered lipocalin (Anticalin) in complex with VEGF(8-109)
6Z13 1.8 Å, VEGF-A 13:107 crystallized with 3C bicyclic peptide
6ZCD 1.8 Å, VEGF-A 13:107 crystallized with 1C bicyclic peptide
3QTK 1.85 Å, The crystal structure of chemically synthesized VEGF-A

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