1BJ1: Vascular endothelial growth factor

Vascular endothelial growth factor in complex with a neutralizing antibody. Determined by X-ray diffraction at 2.4 Å resolution. Released 13 Jan 1999.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Mus musculus, Homo sapiens
Chains: 6
Atoms: 8,694
Mol. weight: 120.81 kDa
Released: 13 Jan 1999

Explore 1BJ1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1BJ1 contains 38 α-helices and 108 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 H: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	10-12	3	7
β-strand	18-25	8	6
α-helix	29-31	3
β-strand	32	1	8
β-strand	34-39	6	7
β-strand	46-51	6	7
β-strand	58-60	3	7
α-helix	62-64	3
β-strand	68-73	6	6
α-helix	74-76	3
β-strand	78-83	6	6
α-helix	88-90	3
β-strand	92-98	7	7
α-helix	99-101	3
β-strand	102-103	2	8
β-strand	105	1	8
β-strand	112-113	2	7
β-strand	117-121	5	7
α-helix	125-126	2
β-strand	127	1	9
β-strand	130-134	5	10
β-strand	145-155	11	10
β-strand	156	1	9
β-strand	161-164	4	11
α-helix	165-167	3
β-strand	173-175	3	10
α-helix	176-178	3
β-strand	179-180	2	10
β-strand	186-195	10	10
β-strand	205-210	6	11
α-helix	211-213	3
β-strand	215-220	6	11

Chain J: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	17
β-strand	10-13	4	18
β-strand	19-25	7	17
β-strand	33-38	6	18
β-strand	45-49	5	18
β-strand	53-54	2	18
α-helix	55	1
β-strand	62-67	6	17
β-strand	70-75	6	17
α-helix	80-82	3
β-strand	84-90	7	18
α-helix	96	1
β-strand	97-98	2	18
β-strand	102-106	5	18
β-strand	111	1	19
β-strand	114-118	5	20
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	20
β-strand	140	1	19
β-strand	144-150	7	21
β-strand	154	1	21
β-strand	159-163	5	20
α-helix	164-167	4
β-strand	173-182	10	20
α-helix	183-186	4
β-strand	191-198	8	21
β-strand	205-210	6	21

Chain K: 9 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	22
β-strand	10-12	3	23
β-strand	18-25	8	22
α-helix	29-31	3
β-strand	32	1	14
β-strand	34-39	6	23
β-strand	46-51	6	23
β-strand	58-60	3	23
α-helix	62-64	3
β-strand	68-73	6	22
β-strand	78-83	6	22
α-helix	88-90	3
β-strand	92-98	7	23
α-helix	99-101	3
β-strand	102-103	2	14
β-strand	105	1	14
β-strand	112-113	2	23
β-strand	117-121	5	23
α-helix	125-126	2
β-strand	127	1	24
β-strand	130-134	5	25
β-strand	145-155	11	25
β-strand	156	1	24
β-strand	161-164	4	26
α-helix	165-167	3
β-strand	174-175	2	25
α-helix	176-178	3
β-strand	179-180	2	25
β-strand	186-195	10	25
α-helix	197-200	4
β-strand	204-209	6	26
β-strand	210	1	27
α-helix	211-213	3
β-strand	215	1	27
β-strand	218-221	4	26

Chain L: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-90	7	2
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-106	5	2
β-strand	111	1	3
α-helix	112-113	2
β-strand	114-118	5	4
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	145-150	6	5
β-strand	153-154	2	5
α-helix	155	1
β-strand	159-163	5	4
α-helix	164-167	4
β-strand	173-182	10	4
α-helix	183-186	4
β-strand	191-197	7	5
β-strand	205-210	6	5

Chains V and W: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	8
α-helix	17-24	8
β-strand	25	1	12
β-strand	27-34	8	13
α-helix	35-38	4
β-strand	46-48	3	14
β-strand	51-58	8	13
β-strand	60	1	12
β-strand	66-84	19	14
β-strand	88-106	19	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab fragment, light chain	J, L	protein	214	Mus musculus
Fab fragment, heavy chain	H, K	protein	231	Mus musculus
Vascular endothelial growth factor A	V, W	protein	102	Homo sapiens	P15692 (AlphaFold model)

Sequence of entity 1 (J, L), FASTA

>1BJ1_1 Fab fragment, light chain (chains J, L)
DIQMTQSPSSLSASVGDRVTITCSASQDISNYLNWYQQKPGKAPKVLIYFTSSLHSGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQQYSTVPWTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (H, K), FASTA

>1BJ1_2 Fab fragment, heavy chain (chains H, K)
EVQLVESGGGLVQPGGSLRLSCAASGYTFTNYGMNWVRQAPGKGLEWVGWINTYTGEPTY
AADFKRRFTFSLDTSKSTAYLQMNSLRAEDTAVYYCAKYPHYYGSSHWYFDVWGQGTLVT
VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Sequence of entity 3 (V, W), FASTA

>1BJ1_3 Vascular endothelial growth factor A (chains V, W)
GQNHHEVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLE
CVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPKKD

Primary citation

VEGF and the Fab fragment of a humanized neutralizing antibody: crystal structure of the complex at 2.4 A resolution and mutational analysis of the interface. Muller, Y.A., Chen, Y., Christinger, H.W. et al. Structure (1998) 6:1153-1167. DOI 10.1016/S0969-2126(98)00116-6 · 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

Browse more

1BJ1 is part of these collections:

Antibodies and the immune system

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