2X1X: Vegf-C

Crystal structure of vegf-C in complex with domains 2 and 3 of VEGFR2 in a tetragonal crystal form. Determined by X-ray diffraction at 3.1 Å resolution. Released 9 Feb 2010.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 2,488
Mol. weight: 38.74 kDa
Ligands: NAG, HG
Released: 9 Feb 2010

Explore 2X1X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2X1X contains 8 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 E: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	114-128	15
β-strand	132-139	8	1
α-helix	140	1
α-helix	141-145	5
β-strand	150-153	4	2
β-strand	156-163	8	1
β-strand	171-189	19	2
β-strand	197-213	17	2

Chain R: 5 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	125	1	3
β-strand	133-138	6	4
α-helix	139	1
α-helix	141	1
β-strand	145-148	4	5
β-strand	152	1	3
β-strand	159-164	6	4
β-strand	168-170	3	4
β-strand	178-180	3	5
β-strand	184-188	5	5
α-helix	189-191	3
β-strand	197-202	6	4
β-strand	209-210	2	4
β-strand	213-218	6	4
β-strand	223-229	7	6
β-strand	234-237	4	7
α-helix	240-241	2
β-strand	242-250	9	6
β-strand	257-261	5	7
β-strand	270-277	8	6
β-strand	286-294	9	6
α-helix	299-301	3
β-strand	303-311	9	7
β-strand	314-325	12	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vascular endothelial growth factor C	E	protein	110	HOMO SAPIENS	P49767 (AlphaFold model)
Vascular endothelial growth factor receptor 2	R	protein	213	HOMO SAPIENS	P35968 (AlphaFold model)

Sequence of entity 1 (E), FASTA

>2X1X_1 VASCULAR ENDOTHELIAL GROWTH FACTOR C (chains E)
AHYNTEILKSIDNEWRKTQCMPREVAIDVGKEFGVATNTFFKPPCVSVYRCGGCCNSEGL
QCMNTSTSYLSKTLFEITVPLSQGPKPVTISFANHTSCRCMSKLHHHHHH

Sequence of entity 2 (R), FASTA

>2X1X_2 VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2 (chains R)
DYRSPFIASVSDQHGVVYITENKNKTVVIPCLGSISNLNVSLCARYPEKRFVPDGNRISW
DSKKGFTIPSYMISYAGMVFCEAKINDESYQSIMYIVVVVGYRIYDVVLSPSHGIELSVG
EKLVLNCTARTELNVGIDFNWEYPSSKHQHKKLVNRDLKTQSGSEMKKFLSTLTIDGVTR
SDQGLYTCAASSGLMTKKNSTFVRVHEDPIEGR

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
HG	Mercury (II) ion	Hg	1

Primary citation

Structural Determinants of Growth Factor Binding and Specificity by Vegf Receptor 2. Leppanen, V.-M., Prota, A.E., Jeltsch, M. et al. Proc Natl Acad Sci U S A (2010) 107:2425. DOI 10.1073/PNAS.0914318107 · PubMed

Other PDB entries of the same protein (UniProt P49767 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6TJT 1.31 Å, Neuropilin2-b1 domain in a complex with the C-terminal VEGFC peptide
2X1W 2.7 Å, Crystal Structure of VEGF-C in Complex with Domains 2 and 3 of VEGFR2
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…
4BSK 4.2 Å, Crystal structure of VEGF-C in complex with VEGFR-3 domains D1-2

Browse structure collections

About this viewer

MolViewer shows 2X1X directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.