5HHD: Vascular endothelial growth factor A

Crystal Structure of Chemically Synthesized Heterochiral {RFX037 plus VEGF-A} Protein Complex in space group P21. Determined by X-ray diffraction at 2.1 Å resolution. Released 9 Mar 2016.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: Homo sapiens, synthetic construct
Chains: 8
Atoms: 5,617
Mol. weight: 79.5 kDa
Released: 9 Mar 2016

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

Secondary structure: helices and β-sheets

5HHD contains 14 α-helices and 48 β-strands across 8 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.

Chains A and B: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	7-8	2	1
α-helix	9	1
α-helix	10-17	8
β-strand	18	1	2
β-strand	20-27	8	3
α-helix	28-31	4
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 C, G and H: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	8-15	8	1
β-strand	20-27	8	1
α-helix	30-42	13
β-strand	47-54	8	1
β-strand	59-64	6	1

Chain D: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	8-15	8	4
β-strand	20-27	8	4
α-helix	30-44	15
β-strand	47-54	8	4
β-strand	59-64	6	4

Chains E and F: 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	59-77	19	10
β-strand	81-99	19	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vascular endothelial growth factor A	A, B	protein	102	Homo sapiens	P15692 (AlphaFold model)
D-Peptide RFX037.D	C, D	protein	69	synthetic construct
D-Vascular endothelial growth factor	E, F	protein	102	synthetic construct
L-Peptide RFX037.L	G, H	protein	69	synthetic construct

Sequence of entity 1 (A, B), FASTA

>5HHD_1 Vascular endothelial growth factor A (chains A, B)
GQNHHEVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLE
CVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPKKD

Sequence of entity 2 (C, D), FASTA

>5HHD_2 D-Peptide RFX037.D (chains C, D)
RRRRRGGSTYKLILNGKTLKGETTTEAVDVFDAFDVFFVYAASNFSDFDDWTYDDATKTF
TVTEGGSDK

Sequence of entity 3 (E, F), FASTA

>5HHD_3 D-Vascular endothelial growth factor (chains E, F)
GQNHHEVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLE
CVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPKKD

Sequence of entity 4 (G, H), FASTA

>5HHD_4 L-Peptide RFX037.L (chains G, H)
RRRRRGGSTYKLILNGKTLKGETTTEAVDVFDAFDVFFVYAASNFSDFDDWTYDDATKTF
TVTEGGSDK

Primary citation

A Potent d-Protein Antagonist of VEGF-A is Nonimmunogenic, Metabolically Stable, and Longer-Circulating in Vivo. Uppalapati, M., Lee, D.J., Mandal, K. et al. ACS Chem Biol (2016) 11:1058-1065. DOI 10.1021/acschembio.5b01006 · 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

Browse structure collections

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