3QTK: Chemically synthesized VEGF-A

The crystal structure of chemically synthesized VEGF-A. Determined by X-ray diffraction at 1.85 Å resolution. Released 27 Jul 2011.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: Homo sapiens
Chains: 6
Atoms: 5,274
Mol. weight: 73.22 kDa
Ligands: TFA
Released: 27 Jul 2011

Explore 3QTK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3QTK contains 16 α-helices and 48 β-strands across 6 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	8	1	1
α-helix	10-17	8
β-strand	18	1	2
β-strand	20-27	8	3
α-helix	28-31	4
α-helix	33-35	3
β-strand	39-41	3	4
β-strand	44-51	8	3
β-strand	53	1	2
β-strand	59-77	19	4
β-strand	81-99	19	4

Chains B and C: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	7
α-helix	10-17	8
β-strand	18	1	8
β-strand	20-27	8	9
α-helix	28-31	4
β-strand	39-41	3	10
β-strand	44-51	8	9
β-strand	53	1	8
β-strand	59-76	18	10
β-strand	82-99	18	10

Chain D: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	4
α-helix	10-17	8
β-strand	18	1	5
β-strand	20-27	8	6
α-helix	28-31	4
β-strand	39-41	3	1
β-strand	44-51	8	6
β-strand	53	1	5
β-strand	59-77	19	1
β-strand	81-99	19	1

Chain E: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7	1
β-strand	8	1	13
α-helix	9	1
α-helix	10-17	8
β-strand	18	1	14
β-strand	20-27	8	15
α-helix	28-31	4
β-strand	39-41	3	16
β-strand	44-51	8	15
β-strand	53	1	14
β-strand	59-76	18	16
β-strand	82-99	18	16

Chain F: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	7-8	2	16
α-helix	10-17	8
β-strand	18	1	17
β-strand	20-27	8	18
α-helix	28-31	4
α-helix	38	1
β-strand	39-41	3	13
β-strand	44-51	8	18
β-strand	53	1	17
β-strand	59-76	18	13
β-strand	83-99	17	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vascular endothelial growth factor A	A, B, C, D, E, F	protein	102	Homo sapiens	P15692 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>3QTK_1 Vascular endothelial growth factor A (chains A, B, C, D, E, F)
GQNHHEVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLE
CVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPKKD

Ligands and cofactors

ID	Name	Formula	Copies
TFA	trifluoroacetic acid	C2 H F3 O2	6

Water and common crystallization additives (GOL, ACT) are not listed.

Primary citation

Total chemical synthesis of biologically active vascular endothelial growth factor. Mandal, K., Kent, S.B. Angew Chem Int Ed Engl (2011) 50:8029-8033. DOI 10.1002/anie.201103237 · 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
6ZCD 1.8 Å, VEGF-A 13:107 crystallized with 1C bicyclic peptide

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