2X1W: VEGF-C

Crystal Structure of VEGF-C in Complex with Domains 2 and 3 of VEGFR2. Determined by X-ray diffraction at 2.7 Å resolution. Released 9 Mar 2010.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: HOMO SAPIENS
Chains: 8
Atoms: 9,720
Mol. weight: 153.99 kDa
Ligands: NAG, CS
Released: 9 Mar 2010

Explore 2X1W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2X1W contains 20 α-helices and 97 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.

Chain A: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
α-helix	117-129	13
β-strand	132-139	8	1
β-strand	151-153	3	2
β-strand	156-163	8	1
β-strand	172-188	17	2
β-strand	197-212	16	2

Chains B and C: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	120-129	10
β-strand	132-139	8	3
α-helix	140-143	4
β-strand	150-153	4	4
β-strand	156-163	8	3
β-strand	171-189	19	4
β-strand	197-213	17	4

Chain D: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	118-129	12
β-strand	132-139	8	7
α-helix	140-143	4
β-strand	150-153	4	8
β-strand	156-163	8	7
β-strand	171-189	19	8
β-strand	197-213	17	8

Chain L: 4 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	125	1	9
α-helix	126-127	2
β-strand	134-138	5	10
β-strand	145-148	4	11
β-strand	152	1	9
β-strand	159-164	6	10
β-strand	168-170	3	10
β-strand	178-180	3	11
β-strand	184-188	5	11
α-helix	189-191	3
β-strand	197-202	6	10
β-strand	209-210	2	10
β-strand	214-218	5	10
β-strand	220	1	12
β-strand	223-229	7	13
β-strand	234-237	4	14
α-helix	240-241	2
β-strand	242-250	9	13
β-strand	254	1	12
β-strand	257-261	5	14
β-strand	270-277	8	13
β-strand	286-294	9	13
α-helix	299-301	3
β-strand	303-310	8	14
β-strand	315-325	11	14

Chain M: 3 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	135-138	4	15
β-strand	145-148	4	16
β-strand	160-164	5	15
β-strand	168-170	3	15
β-strand	178-179	2	16
β-strand	185-188	4	16
α-helix	189-191	3
β-strand	197-201	5	15
β-strand	214-218	5	15
β-strand	223-229	7	17
β-strand	235-237	3	18
α-helix	240-241	2
β-strand	242-251	10	17
β-strand	257-261	5	19
β-strand	270-277	8	17
β-strand	285-294	10	17
α-helix	299-301	3
β-strand	303-310	8	19
β-strand	315-322	8	19
β-strand	323-325	3	18

Chain N: 3 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	125	1	20
β-strand	134-138	5	21
β-strand	145-148	4	22
β-strand	152	1	20
β-strand	159-164	6	21
β-strand	168-170	3	21
β-strand	178-179	2	22
β-strand	185-188	4	22
α-helix	189-191	3
β-strand	197-204	8	21
β-strand	207-210	4	21
β-strand	214-218	5	21
β-strand	223-229	7	23
β-strand	235-237	3	24
α-helix	240-241	2
β-strand	242-251	10	23
β-strand	257-261	5	25
β-strand	271-277	7	23
β-strand	285-294	10	23
α-helix	299-301	3
β-strand	303-310	8	25
β-strand	315-322	8	25
β-strand	323-325	3	24

Chain O: 3 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	125	1	26
β-strand	133-138	6	27
β-strand	145-148	4	28
β-strand	152	1	26
β-strand	158-164	7	27
β-strand	168-170	3	27
β-strand	178-180	3	28
β-strand	184-188	5	28
α-helix	189-191	3
β-strand	197-203	7	27
β-strand	208-210	3	27
β-strand	213-218	6	27
β-strand	223-229	7	29
β-strand	234-236	3	30
α-helix	240-241	2
β-strand	242-250	9	29
β-strand	257-261	5	30
β-strand	270-277	8	29
β-strand	286-294	9	29
α-helix	299-301	3
β-strand	303-310	8	30
β-strand	315-324	10	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vascular endothelial growth factor C	A, B, C, D	protein	110	HOMO SAPIENS	P49767 (AlphaFold model)
Vascular endothelial growth factor receptor 2	L, M, N, O	protein	213	HOMO SAPIENS	P35968 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>2X1W_1 VASCULAR ENDOTHELIAL GROWTH FACTOR C (chains A, B, C, D)
AHYNTEILKSIDNEWRKTQCMPREVAIDVGKEFGVATNTFFKPPCVSVYRCGGCCNSEGL
QCMNTSTSYLSKTLFEITVPLSQGPKPVTISFANHTSCRCMSKLHHHHHH

Sequence of entity 2 (L, M, N, O), FASTA

>2X1W_2 VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2 (chains L, M, N, O)
DYRSPFIASVSDQHGVVYITENKNKTVVIPCLGSISNLNVSLCARYPEKRFVPDGNRISW
DSKKGFTIPSYMISYAGMVFCEAKINDESYQSIMYIVVVVGYRIYDVVLSPSHGIELSVG
EKLVLNCTARTELNVGIDFNWEYPSSKHQHKKLVNRDLKTQSGSEMKKFLSTLTIDGVTR
SDQGLYTCAASSGLMTKKNSTFVRVHEDPIEGR

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	7
CS	Cesium ion	Cs	2

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
2X1X 3.1 Å, Crystal structure of vegf-C in complex with domains 2 and 3 of VEGFR2 in a tetragonal…
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

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