4GLN: D-RFX001

Crystal Structure of Chemically Synthesized Heterochiral {D-Protein Antagonist plus VEGF-A} Protein Complex in space group P21/n. Determined by X-ray diffraction at 1.6 Å resolution. Released 5 Sept 2012.

Method: X-ray diffraction
Resolution: 1.6 Å
Organisms: synthetic construct, Homo sapiens
Chains: 4
Atoms: 3,060
Mol. weight: 36.65 kDa
Released: 5 Sept 2012

Explore 4GLN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4GLN contains 11 α-helices and 26 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 D: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	12-17	6	1
α-helix	22-36	15
β-strand	39-40	2	2
β-strand	42-46	5	1
β-strand	51-55	5	1

Chains E and F: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7	1
β-strand	8	1	2
α-helix	9	1
α-helix	10-17	8
β-strand	18	1	3
β-strand	20-27	8	4
α-helix	28-31	4
β-strand	39-41	3	5
β-strand	44-51	8	4
β-strand	53	1	3
β-strand	59-77	19	5
β-strand	81-99	19	5

Chain H: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	8
β-strand	12-17	6	8
α-helix	22-36	15
β-strand	39-40	2	5
β-strand	42-46	5	8
α-helix	47-49	3
β-strand	51-55	5	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
D-RFX001	D, H	protein	56	synthetic construct
Vascular endothelial growth factor A	E, F	protein	102	Homo sapiens	P15692 (AlphaFold model)

Sequence of entity 1 (D, H), FASTA

>4GLN_1 D-RFX001 (chains D, H)
TYKLILNGKTLKGETTTEAVDVFDAFDVFFVYAASNFSDFDDWTYDDATKTFTVTE

Sequence of entity 2 (E, F), FASTA

>4GLN_2 Vascular endothelial growth factor A (chains E, F)
GQNHHEVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLE
CVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPKKD

Primary citation

Chemical synthesis and X-ray structure of a heterochiral {D-protein antagonist plus vascular endothelial growth factor} protein complex by racemic crystallography. Mandal, K., Uppalapati, M., Ault-Riche, D. et al. Proc Natl Acad Sci U S A (2012) 109:14779-14784. DOI 10.1073/pnas.1210483109 · 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
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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