6ZCD: Derived from V114 peptide

VEGF-A 13:107 crystallized with 1C bicyclic peptide. Determined by X-ray diffraction at 1.8 Å resolution. Released 23 Jun 2021.

Method: X-ray diffraction
Resolution: 1.8 Å
Organisms: synthetic construct, Homo sapiens
Chains: 3
Atoms: 1,868
Mol. weight: 24.88 kDa
Ligands: PO4
Released: 23 Jun 2021

Explore 6ZCD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ZCD contains 8 α-helices and 16 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 P: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
α-helix	10-13	4

Chain V: 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 W: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	14-15	2	4
α-helix	17-24	8
β-strand	25	1	5
β-strand	27-34	8	6
α-helix	35-38	4
α-helix	40-42	3
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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Derived from V114 peptide	P	protein	15	synthetic construct
Vascular endothelial growth factor A	V, W	protein	95	Homo sapiens	P15692 (AlphaFold model)

Sequence of entity 1 (P), FASTA

>6ZCD_1 Derived from V114 peptide (chains P)
CDIHVLWEWKCFEDL

Sequence of entity 2 (V, W), FASTA

>6ZCD_2 Vascular endothelial growth factor A (chains V, W)
EVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTE
ESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPK

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1

Water and common crystallization additives (MPD) are not listed.

Primary citation

Structural and ITC Characterization of Peptide-Protein Binding: Thermodynamic Consequences of Cyclization Constraints, a Case Study on Vascular Endothelial Growth Factor Ligands. Gaucher, J.F., Reille-Seroussi, M., Broussy, S. Chemistry (2022). DOI 10.1002/chem.202200465 · 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
9KKU 1.46 Å, Helix-loop-helix peptide (M49) 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
3QTK 1.85 Å, The crystal structure of chemically synthesized VEGF-A

Browse structure collections

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