4BSK: VEGF-C

Crystal structure of VEGF-C in complex with VEGFR-3 domains D1-2. Determined by X-ray diffraction at 4.2 Å resolution. Released 31 Jul 2013.

Method: X-ray diffraction
Resolution: 4.2 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 1,876
Mol. weight: 38.76 kDa
Ligands: NAG
Released: 31 Jul 2013

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

Secondary structure: helices and β-sheets

4BSK contains 4 α-helices and 24 β-strands across 2 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: 2 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	38-42	5	1
β-strand	47-52	6	2
β-strand	58-59	2	3
β-strand	69-70	2	2
β-strand	93-98	6	2
α-helix	103-105	3
β-strand	107-110	4	1
β-strand	111-112	2	3
β-strand	127-133	7	1
β-strand	139-140	2	4
β-strand	154-155	2	5
β-strand	159-160	2	4
β-strand	168-170	3	6
β-strand	175-176	2	6
β-strand	184-186	3	5
β-strand	190-193	4	5
α-helix	195-198	4
β-strand	203	1	7
β-strand	205-207	3	6
β-strand	216	1	6
β-strand	220	1	7

Chain C: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	116-129	14
β-strand	132-139	8	8
α-helix	140-144	5
β-strand	151-153	3	9
β-strand	156-163	8	8
β-strand	173-188	16	9
β-strand	197-211	15	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vascular endothelial growth factor receptor 3	A	protein	214	HOMO SAPIENS	P35916 (AlphaFold model)
Vascular endothelial growth factor C	C	protein	121	HOMO SAPIENS	P49767 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4BSK_1 VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 3 (chains A)
SGYSMTPPTLNITEESHVIDTGDSLSISCRGQHPLEWAWPGAQEAPATGDKDSEDTGVVR
DCEGTDARPYCKVLLLHEVHANDTGSYVCYYKYIKARIEGTTAASSYVFVRDFEQPFINK
PDTLLVNRKDAMWVPCLVSIPGLNVTLRSQSSVLWPDGQEVVWDDRRGMLVSTPLLHDAL
YLQCETTWGDQDFLSNPFLVHITGNELADPIEGR

Sequence of entity 2 (C), FASTA

>4BSK_2 VASCULAR ENDOTHELIAL GROWTH FACTOR C (chains C)
DPTEETIKFAAAHYNTEILKSIDNEWRKTQCMPREVAIDVGKEFGVATNTFFKPPCVSVY
RCGGCCNSEGLQCMNTSTSYLSKTLFEITVPLSQGPKPVTISFANHTSCRCMSKLHHHHH
H

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Primary citation

Structural and Mechanistic Insights Into Vegfr-3 Ligand Binding and Activation. Leppanen, V.-M., Tvorogov, D., Kisko, K. et al. Proc Natl Acad Sci U S A (2013) 110:12960. DOI 10.1073/PNAS.1301415110 · PubMed

Other PDB entries of the same protein (UniProt P35916 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4BSJ 2.5 Å, Crystal structure of VEGFR-3 extracellular domains D4-5
21EI 3.3 Å, Structural and Functional Insights into VEGFR-3-Mediated Lymphangiogenesis : Unraveling…
21ES 3.3 Å, Structural and Functional Insights into VEGFR-3-Mediated Lymphangiogenesis : Unraveling…

Browse structure collections

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