2VPF: Vascular endothelial growth factor

Name: PDB 2VPF: Vascular endothelial growth factor refined to 1.93 Å resolution
Published: 1998-07-29
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: growth factor

Vascular endothelial growth factor refined to 1.93 Å resolution. Determined by X-ray diffraction at 1.93 Å resolution. Released 29 Jul 1998.

Method: X-ray diffraction
Resolution: 1.93 Å
Organism: Homo sapiens
Chains: 8
Atoms: 6,782
Mol. weight: 95.59 kDa
Released: 29 Jul 1998

Explore 2VPF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2VPF contains 28 α-helices and 64 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, B and G: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	14	1
β-strand	15	1	1
α-helix	16	1
α-helix	17-24	8
β-strand	25	1	2
β-strand	27-34	8	3
α-helix	35-38	4
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	89-106	18	4

Chain C: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	7
α-helix	17-23	7
β-strand	25	1	8
β-strand	27-34	8	9
α-helix	35-38	4
β-strand	46-48	3	10
β-strand	51-58	8	9
β-strand	60	1	8
β-strand	67-84	18	10
β-strand	88-105	18	10

Chain D: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	14	1
β-strand	15	1	10
α-helix	16	1
α-helix	17-23	7
β-strand	25	1	11
β-strand	27-34	8	12
α-helix	35-38	4
β-strand	46-48	3	7
β-strand	51-58	8	12
β-strand	60	1	11
β-strand	66-83	18	7
β-strand	89-106	18	7

Chain E: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	14	1
β-strand	15	1	13
α-helix	16	1
α-helix	17-24	8
β-strand	25	1	14
β-strand	27-34	8	15
α-helix	35-38	4
β-strand	46-48	3	16
β-strand	51-58	8	15
β-strand	60	1	14
β-strand	66-84	19	16
β-strand	88-106	19	16

Chain F: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	14	1
β-strand	15	1	16
α-helix	16	1
α-helix	17-24	8
β-strand	25	1	17
β-strand	27-34	8	18
α-helix	35-38	4
β-strand	46-48	3	13
β-strand	51-58	8	18
β-strand	60	1	17
β-strand	66-83	18	13
β-strand	90-106	17	13

Chain H: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	22
α-helix	17-24	8
β-strand	25	1	23
β-strand	27-34	8	24
α-helix	35-38	4
β-strand	46-48	3	19
β-strand	51-58	8	24
β-strand	60	1	23
β-strand	66-83	18	19
β-strand	89-106	18	19

Molecules and chains

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

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

>2VPF_1 VASCULAR ENDOTHELIAL GROWTH FACTOR (chains A, B, C, D, E, F, G, H)
GQNHHEVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLE
CVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPKKD

Primary citation

The crystal structure of vascular endothelial growth factor (VEGF) refined to 1.93 A resolution: multiple copy flexibility and receptor binding. Muller, Y.A., Christinger, H.W., Keyt, B.A. et al. Structure (1997) 5:1325-1338. DOI 10.1016/S0969-2126(97)00284-0 · 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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