2XAC: Vascular endothelial growth factor B

Structural Insights into the Binding of VEGF-B by VEGFR-1D2: Recognition and Specificity. Determined by X-ray diffraction at 2.71 Å resolution. Released 19 May 2010.

Method: X-ray diffraction
Resolution: 2.71 Å
Organism: HOMO SAPIENS
Chains: 4
Atoms: 3,013
Mol. weight: 44.83 kDa
Released: 19 May 2010

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

Secondary structure: helices and β-sheets

2XAC contains 9 α-helices and 37 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 A: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	1
α-helix	16	1
α-helix	19-23	5
β-strand	25	1	2
β-strand	27-34	8	3
α-helix	35-36	2
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	89-105	17	4

Chain B: 3 helices, 9 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	27-34	8	5
β-strand	45-48	4	6
β-strand	51-58	8	5
β-strand	66-75	10	7
β-strand	78	1	1
β-strand	80-84	5	6
β-strand	90-91	2	6
β-strand	96-105	10	7

Chain C: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	135	1	8
β-strand	144-147	4	9
β-strand	154-156	3	10
β-strand	160	1	8
β-strand	168-169	2	9
β-strand	171	1	11
β-strand	174	1	11
β-strand	192-194	3	10
α-helix	199-201	3
β-strand	204-211	8	9
β-strand	214-223	10	9

Chain X: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	135	1	12
α-helix	138-139	2
α-helix	143	1
β-strand	144-147	4	13
β-strand	154-156	3	14
β-strand	160	1	12
β-strand	168-171	4	13
β-strand	175-177	3	13
β-strand	184-187	4	14
β-strand	191-194	4	14
β-strand	203-211	9	13
β-strand	214-223	10	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vascular endothelial growth factor B	A, B	protein	99	HOMO SAPIENS	P49765 (AlphaFold model)
Vascular endothelial growth factor receptor 1	C, X	protein	98	HOMO SAPIENS	P17948 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2XAC_1 VASCULAR ENDOTHELIAL GROWTH FACTOR B (chains A, B)
HQRKVVSWIDVYTRATCQPREVVVPLTVELMGTVAKQLVPSCVTVQRCGGCCPDDGLECV
PTGQHQVRMQILMIRYPSSQLGEMSLEEHSQCECRPKKK

Sequence of entity 2 (C, X), FASTA

>2XAC_2 VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 1 (chains C, X)
SDTGRPFVEMYSEIPEIIHMTEGRELVIPCRVTSPNITVTLKKFPLDTLIPDGKRIIWDS
RKGFIISNATYKEIGLLTCEATVNGHLYKTNYLTHRQT

Primary citation

Structural Insights Into the Binding of Vegf-B by Vegfr-1D2: Recognition and Specificity. Iyer, S., Darley, P., Acharya, K.R. J Biol Chem (2010) 285:23779. DOI 10.1074/JBC.M110.130658 · PubMed

Other PDB entries of the same protein (UniProt P49765 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6TKK 1.06 Å, Neuropilin 1-b1 domain in a complex with the C-terminal VEGFB186 peptide
2C7W 2.48 Å, Crystal Structure of human vascular endothelial growth factor-B: Identification of amino…
2VWE 3.4 Å, Crystal Structure of Vascular Endothelial Growth Factor-B in Complex with a Neutralizing…

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