5ABD: Vegfr-1 domain 2 in presence of CU

Crystal structure of vegfr-1 domain 2 in presence of CU. Determined by X-ray diffraction at 2.0 Å resolution. Released 28 Sept 2016.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: HOMO SAPIENS
Chains: 3
Atoms: 2,541
Mol. weight: 33.28 kDa
Ligands: CU
Released: 28 Sept 2016

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

Secondary structure: helices and β-sheets

5ABD contains 6 α-helices and 30 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.

Chains E and X: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	135	1	1
α-helix	143	1
β-strand	144-148	5	2
β-strand	154-156	3	3
β-strand	160	1	1
β-strand	167-171	5	2
β-strand	175-177	3	2
β-strand	184-187	4	3
β-strand	191-194	4	3
α-helix	199-201	3
β-strand	203-211	9	2
β-strand	214-224	11	2

Chain I: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	135	1	4
α-helix	143	1
β-strand	144-147	4	5
β-strand	154-156	3	6
β-strand	160	1	4
β-strand	167-171	5	5
β-strand	175-176	2	5
β-strand	184-187	4	6
β-strand	191-194	4	6
α-helix	199-201	3
β-strand	203-211	9	5
β-strand	214-223	10	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vascular endothelial growth factor receptor 1	E, I, X	protein	95	HOMO SAPIENS	P17948 (AlphaFold model)

Sequence of entity 1 (E, I, X), FASTA

>5ABD_1 VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 1 (chains E, I, X)
GRPFVEMYSEIPEIIHMTEGRELVIPCRVTSPNITVTLKKFPLDTLIPDGKRIIWDSRKG
FIISNATYKEIGLLTCEATVNGHLYKTNYLTHRQT

Ligands and cofactors

ID	Name	Formula	Copies
CU	Copper (II) ion	Cu	5

Water and common crystallization additives (NA, SO4) are not listed.

Primary citation

Biophysical Studies of the Induced Dimerization of Human Vegf R Receptor 1 Binding Domain by Divalent Metals Competing with Vegf-A. Gaucher, J.-F., Reille-Seroussi, M., Gagey-Eilstein, N. et al. PLoS One (2016) 11:67755. DOI 10.1371/JOURNAL.PONE.0167755 · PubMed

Other PDB entries of the same protein (UniProt P17948 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1FLT 1.7 Å, Vegf in complex with domain 2 of the flt-1 receptor
4CL7 2.0 Å, Crystal structure of VEGFR-1 domain 2 in presence of Cobalt
4CKV 2.06 Å, Crystal structure of VEGFR-1 domain 2 in presence of Zn
5EX3 2.41 Å, Crystal structure of human SMYD3 in complex with a VEGFR1 peptide
1RV6 2.45 Å, Crystal Structure of PlGF in Complex with Domain 2 of VEGFR1
1QTY 2.7 Å, Vascular endothelial growth factor in complex with domain 2 of the flt-1 receptor
3HNG 2.7 Å, Crystal structure of VEGFR1 in complex with N-(4-Chlorophenyl)-2-((pyridin-4-ylmethyl)ami…
2XAC 2.71 Å, Structural Insights into the Binding of VEGF-B by VEGFR-1D2: Recognition and Specificity
5T89 4.0 Å, Crystal structure of VEGF-A in complex with VEGFR-1 domains D1-6
1QSV The vegf-binding domain of flt-1, 20 NMR structures
1QSZ The vegf-binding domain of flt-1 (minimized mean)

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