2VWE: Vascular Endothelial Growth Factor-B

Crystal Structure of Vascular Endothelial Growth Factor-B in Complex with a Neutralizing Antibody Fab Fragment. Determined by X-ray diffraction at 3.4 Å resolution. Released 4 Nov 2008.

Method: X-ray diffraction
Resolution: 3.4 Å
Organisms: HOMO SAPIENS, MUS MUSCULUS
Chains: 6
Atoms: 8,109
Mol. weight: 132.36 kDa
Released: 4 Nov 2008

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

Secondary structure: helices and β-sheets

2VWE contains 22 α-helices and 98 β-strands across 6 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, 6 β-strands

Element	Residues	Length	Sheet
β-strand	14-15	2	1
α-helix	17-24	8
β-strand	27-34	8	2
β-strand	47-48	2	3
β-strand	51-58	8	2
β-strand	66-82	17	3
β-strand	89-105	17	3

Chain B: 1 helix, 6 β-strands

Element	Residues	Length	Sheet
β-strand	14-15	2	3
α-helix	17-24	8
β-strand	27-34	8	4
β-strand	46-48	3	1
β-strand	51-58	8	4
β-strand	66-83	18	1
β-strand	89-105	17	1

Chain C: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	5
β-strand	10-13	4	6
β-strand	19-25	7	5
β-strand	33-38	6	6
β-strand	44-48	5	6
β-strand	54	1	6
β-strand	62-65	4	5
β-strand	70-75	6	5
α-helix	80-82	3
β-strand	85-90	6	6
β-strand	98	1	6
β-strand	102-106	5	6
β-strand	110	1	7
β-strand	114-117	4	8
α-helix	118-120	3
α-helix	121-124	4
β-strand	128-138	11	8
β-strand	139	1	7
β-strand	144-149	6	9
β-strand	152-154	3	9
β-strand	158-162	5	8
α-helix	163-166	4
β-strand	172-181	10	8
α-helix	182-185	4
β-strand	190-196	7	9
α-helix	203	1
β-strand	204-209	6	9

Chain E: 5 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	10
β-strand	9-12	4	6
β-strand	18-25	8	10
α-helix	29-31	3
β-strand	33-39	7	6
β-strand	46-52	7	6
β-strand	56-59	4	6
β-strand	65	1	11
β-strand	67	1	11
β-strand	68-72	5	10
β-strand	77-82	6	10
α-helix	84-86	3
β-strand	89-95	7	6
β-strand	100C-103	4	6
β-strand	107-111	5	6
α-helix	114-116	3
β-strand	117	1	12
β-strand	120-123	4	13
α-helix	125-127	3
β-strand	135-137	3	14
β-strand	140-145	6	13
β-strand	146	1	12
β-strand	151-154	4	15
β-strand	163-165	3	13
α-helix	166-168	3
β-strand	169-171	3	13
β-strand	174-181	8	13
β-strand	182-184	3	14
β-strand	194-198	5	15
β-strand	208-209	2	15

Chain J: 5 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	16
β-strand	10-13	4	17
β-strand	19-24	6	16
β-strand	33-38	6	17
β-strand	44-48	5	17
β-strand	54	1	17
α-helix	55	1
β-strand	62-66	5	16
β-strand	70-75	6	16
β-strand	85-90	6	17
β-strand	98	1	17
β-strand	102-106	5	17
β-strand	115-117	3	18
α-helix	118-120	3
α-helix	121-124	4
β-strand	129-138	10	18
β-strand	144-149	6	19
β-strand	152-153	2	19
β-strand	158-162	5	18
α-helix	163-166	4
β-strand	172-180	9	18
α-helix	182-185	4
β-strand	191-197	7	19
β-strand	200-208	9	19

Chain L: 4 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	20
β-strand	9-12	4	17
β-strand	18-25	8	20
α-helix	29-31	3
β-strand	33-39	7	17
β-strand	45-51	7	17
β-strand	57-59	3	17
α-helix	61-63	3
β-strand	67-72	6	20
β-strand	77-82	6	20
α-helix	84-86	3
β-strand	89-95	7	17
β-strand	100C-103	4	17
β-strand	107-111	5	17
β-strand	120-123	4	21
β-strand	135-137	3	22
β-strand	140-145	6	21
β-strand	151-154	4	23
β-strand	163-165	3	21
α-helix	166-168	3
β-strand	169-171	3	21
β-strand	174-181	8	21
β-strand	182-184	3	22
β-strand	193-198	6	23
β-strand	208-210	3	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vascular endothelial growth factor B	A, B	protein	167	HOMO SAPIENS	P49765 (AlphaFold model)
Anti-vegf-B monoclonal antibody	C, J	protein	214	MUS MUSCULUS	P01647 (AlphaFold model), P01837 (AlphaFold model)
Anti-vegf-B monoclonal antibody	E, L	protein	219	MUS MUSCULUS	P01864 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2VWE_1 VASCULAR ENDOTHELIAL GROWTH FACTOR B (chains A, B)
PVSQPDAPGHQRKVVSWIDVYTRATCQPREVVVPLTVELMGTVAKQLVPSCVTVQRCGGC
CPDDGLECVPTGQHQVRMQILMIRYPSSQLGEMSLEEHSQCECRPKKKDSAVKPDSPRPL
CPRCTQHHQRPDPRTCRCRCRRRSFLRCQGRGLELNPDTCRCRKLRR

Sequence of entity 2 (C, J), FASTA

>2VWE_2 ANTI-VEGF-B MONOCLONAL ANTIBODY (chains C, J)
EIQMTQTTSSLSASLGDRVTISCRASQDISNFLNWYQQKPDGTVKLLIYYTSTLHSGVPS
RFSGSGSGTDYSLTISNLEQEDIATYFCQQGKTLPPTFGGGTKLEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKEINVKWKIDGSERQNGVLDSWTEQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 3 (E, L), FASTA

>2VWE_3 ANTI-VEGF-B MONOCLONAL ANTIBODY (chains E, L)
QVQLQQPGTELVKPGASVKLSCKASGYTFTGFWIHWVKQRPGQGLEWIGHINPGNGGTNY
NEKFKRMATLTVDKSSSTAYMQLSSLTSEDSAVYYCARSYSNYVRAMDYWGQGTSVTVSS
AKTTAPSVYPLVPVCGGTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPALLQSG
LYTLSSSVTVTSNTWPSQTITCNVAHPASSTKVDKKIEP

Primary citation

Crystal Structure of Vascular Endothelial Growth Factor-B in Complex with a Neutralising Antibody Fab Fragment. Leonard, P., Scotney, P.D., Jabeen, T. et al. J Mol Biol (2008) 384:1203. DOI 10.1016/J.JMB.2008.09.076 · 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…
2XAC 2.71 Å, Structural Insights into the Binding of VEGF-B by VEGFR-1D2: Recognition and Specificity

Browse structure collections

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