5T89: VEGF-A

Crystal structure of VEGF-A in complex with VEGFR-1 domains D1-6. Determined by X-ray diffraction at 4.0 Å resolution. Released 1 Feb 2017.

Method: X-ray diffraction
Resolution: 4.0 Å
Organism: Homo sapiens
Chains: 4
Atoms: 11,357
Mol. weight: 182.19 kDa
Ligands: NAG
Released: 1 Feb 2017

Explore 5T89 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5T89 contains 21 α-helices and 122 β-strands across 4 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 V: 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 W: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	14	1
β-strand	15	1	4
α-helix	16	1
α-helix	17-22	6
β-strand	25	1	5
β-strand	27-34	8	6
α-helix	35-38	4
β-strand	46-48	3	1
β-strand	51-58	8	6
β-strand	60	1	5
β-strand	66-83	18	1
β-strand	89-106	18	1

Chain X: 7 helices, 51 β-strands

Element	Residues	Length	Sheet
β-strand	33-34	2	7
β-strand	50-55	6	7
β-strand	60-62	3	8
β-strand	73-75	3	7
β-strand	88-93	6	7
β-strand	103-108	6	8
α-helix	113-115	3
β-strand	121-126	6	8
β-strand	135	1	9
α-helix	143	1
β-strand	144-148	5	10
β-strand	154-156	3	11
β-strand	160	1	9
β-strand	167-171	5	10
β-strand	175-177	3	10
α-helix	178-179	2
β-strand	184-187	4	11
β-strand	191-194	4	11
α-helix	199-201	3
β-strand	204-211	8	10
β-strand	214-224	11	10
β-strand	231-235	5	12
β-strand	240-241	2	13
β-strand	248-256	9	12
β-strand	264-267	4	13
β-strand	276-282	7	12
β-strand	290-298	9	12
α-helix	303-305	3
β-strand	307-314	8	13
β-strand	319-327	9	13
β-strand	333-336	4	14
β-strand	344-347	4	15
β-strand	351-356	6	16
β-strand	359-362	4	14
β-strand	366-369	4	15
β-strand	373	1	15
β-strand	389-394	6	16
α-helix	397-399	3
β-strand	401-409	9	15
β-strand	414-425	12	15
β-strand	429-430	2	17
α-helix	431-433	3
β-strand	443-444	2	18
β-strand	450-451	2	17
β-strand	454-457	4	17
β-strand	463-466	4	19
β-strand	501-512	12	17
β-strand	515-526	12	17
β-strand	531-538	8	19
β-strand	543-550	8	19
β-strand	551-552	2	18
β-strand	560-564	5	20
β-strand	573-579	7	20
β-strand	588-592	5	21
β-strand	617-623	7	20
β-strand	632-638	7	21
β-strand	646-648	3	21
β-strand	651-652	2	21

Chain Y: 6 helices, 55 β-strands

Element	Residues	Length	Sheet
β-strand	33-34	2	22
β-strand	43	1	23
β-strand	50-55	6	22
β-strand	60-62	3	24
β-strand	73-75	3	22
β-strand	88-93	6	22
α-helix	99-101	3
β-strand	103-108	6	24
β-strand	121-126	6	24
β-strand	128	1	23
β-strand	135	1	25
α-helix	143	1
β-strand	144-148	5	26
β-strand	154-156	3	27
β-strand	160	1	25
β-strand	167-171	5	26
β-strand	176-177	2	26
α-helix	178-179	2
β-strand	184-187	4	27
β-strand	191-194	4	27
α-helix	199-201	3
β-strand	204-211	8	26
β-strand	214-224	11	26
β-strand	231-235	5	28
β-strand	240-241	2	29
β-strand	248-256	9	28
β-strand	263-267	5	29
β-strand	276-282	7	28
β-strand	290-298	9	28
β-strand	307-314	8	29
β-strand	319-327	9	29
β-strand	333-336	4	30
β-strand	344-347	4	31
β-strand	351-356	6	32
β-strand	359-362	4	30
β-strand	366-369	4	31
β-strand	373	1	31
β-strand	384	1	32
β-strand	389-394	6	32
α-helix	397-399	3
β-strand	401-409	9	31
β-strand	414-425	12	31
β-strand	430	1	33
α-helix	431-433	3
β-strand	445	1	34
β-strand	450-456	7	33
β-strand	464-466	3	35
β-strand	501-512	12	33
β-strand	515-526	12	33
β-strand	531-539	9	35
β-strand	542-550	9	35
β-strand	553	1	34
β-strand	560-564	5	36
β-strand	573-579	7	36
β-strand	585-591	7	37
β-strand	595	1	38
β-strand	598	1	38
β-strand	611	1	36
β-strand	617-623	7	36
β-strand	633-639	7	37
β-strand	647-651	5	37

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vascular endothelial growth factor A	V, W	protein	131	Homo sapiens	P15692 (AlphaFold model)
Vascular endothelial growth factor receptor 1	X, Y	protein	646	Homo sapiens	P17948 (AlphaFold model)

Sequence of entity 1 (V, W), FASTA

>5T89_1 Vascular endothelial growth factor A (chains V, W)
GSHHHHHHGSAPMAEGGGQNHHEVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPS
CVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPKKDR
ARQENCDKPRR

Sequence of entity 2 (X, Y), FASTA

>5T89_2 Vascular endothelial growth factor receptor 1 (chains X, Y)
SKLKDPELSLKGTQHIMQAGQTLHLQCRGEAAHKWSLPEMVSKESERLSITKSACGRNGK
QFCSTLTLNTAQANHTGFYSCKYLAVPTSKKKETESAIYIFISDTGRPFVEMYSEIPEII
HMTEGRELVIPCRVTSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLT
CEATVNGHLYKTNYLTHRQTNTIIDVQISTPRPVKLLRGHTLVLNCTATTPLNTRVQMTW
SYPDEKNKRASVRRRIDQSNSHANIFYSVLTIDKMQNKDKGLYTCRVRSGPSFKSVNTSV
HIYDKAFITVKHRKQQVLETVAGKRSYRLSMKVKAFPSPEVVWLKDGLPATEKSARYLTR
GYSLIIKDVTEEDAGNYTILLSIKQSNVFKNLTATLIVNVKPQIYEKAVSSFPDPALYPL
GSRQILTCTAYGIPQPTIKWFWHPCNHNHSEARCDFCSNNEESFILDADSNMGNRIESIT
QRMAIIEGKNKMASTLVVADSRISGIYICIASNKVGTVGRNISFYITDVPNGFHVNLEKM
PTEGEDLKLSCTVNKFLYRDVTWILLRTVNNRTMHYSISKQKMAITKEHSITLNLTIMNV
SLQDSGTYACRARNVYTGEEILQKKEITIRDQEAIEGRHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	19

Primary citation

Structure of the Full-length VEGFR-1 Extracellular Domain in Complex with VEGF-A. Markovic-Mueller, S., Stuttfeld, E., Asthana, M. et al. Structure (2017) 25:341-352. DOI 10.1016/j.str.2016.12.012 · 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

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