6BFT: Bevacizumab Fab mutant

Structure of Bevacizumab Fab mutant in complex with VEGF. Determined by X-ray diffraction at 2.55 Å resolution. Released 31 Oct 2018.

Method: X-ray diffraction
Resolution: 2.55 Å
Organism: Homo sapiens
Chains: 6
Atoms: 8,359
Mol. weight: 121.34 kDa
Released: 31 Oct 2018

Explore 6BFT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6BFT contains 47 α-helices and 107 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: 12 helices, 25 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	45-51	7	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	1	8
β-strand	112-113	2	7
β-strand	114	1	6
β-strand	117-121	5	7
α-helix	124-126	3
β-strand	127	1	9
α-helix	128-129	2
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	169	1	11
β-strand	173-175	3	10
α-helix	176-178	3
β-strand	179-180	2	10
β-strand	186-195	10	10
α-helix	196-198	3
β-strand	205-210	6	11
α-helix	211-213	3
β-strand	215-220	6	11
α-helix	223-225	3

Chain B: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	1
β-strand	10-14	5	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	102-107	6	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	183-188	6
β-strand	191-197	7	5
β-strand	205-210	6	5

Chain C: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	8
α-helix	17-24	8
β-strand	25	1	25
β-strand	27-34	8	26
α-helix	35-38	4
α-helix	45	1
β-strand	46-48	3	19
β-strand	51-58	8	26
β-strand	60	1	25
β-strand	66-84	19	19
β-strand	88-106	19	19

Chain G: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	14-15	2	19
α-helix	16	1
α-helix	17-24	8
β-strand	25	1	23
β-strand	27-34	8	24
α-helix	35-38	4
β-strand	46-48	3	8
β-strand	51-58	8	24
β-strand	60	1	23
β-strand	66-84	19	8
β-strand	88-106	19	8

Chain H: 10 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	17
β-strand	10-12	3	18
β-strand	18-25	8	17
α-helix	29-31	3
β-strand	34-39	6	18
β-strand	46-51	6	18
β-strand	58-60	3	18
α-helix	62-64	3
β-strand	68-73	6	17
α-helix	74-76	3
β-strand	78-83	6	17
α-helix	88-90	3
β-strand	92-98	7	18
α-helix	99-101	3
β-strand	102-103	2	19
β-strand	105	1	19
β-strand	112-113	2	18
β-strand	117-121	5	18
α-helix	125-126	2
β-strand	127	1	20
α-helix	128-129	2
β-strand	130-134	5	21
β-strand	145-155	11	21
β-strand	156	1	20
β-strand	161-164	4	22
α-helix	165-167	3
β-strand	169	1	22
β-strand	173-175	3	21
β-strand	179-180	2	21
β-strand	186-195	10	21
α-helix	198-201	4
β-strand	204-210	7	22
α-helix	211-213	3
β-strand	215-221	7	22

Chain L: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-14	5	13
β-strand	19-25	7	12
β-strand	33-38	6	13
β-strand	45-49	5	13
β-strand	53-54	2	13
α-helix	55	1
β-strand	62-67	6	12
β-strand	70-75	6	12
α-helix	80-82	3
β-strand	84-90	7	13
α-helix	96	1
β-strand	97-98	2	13
β-strand	102-107	6	13
β-strand	111	1	14
α-helix	112-113	2
β-strand	114-118	5	15
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	15
β-strand	140	1	14
β-strand	145-150	6	16
β-strand	153-154	2	16
α-helix	155	1
β-strand	159-163	5	15
α-helix	164-167	4
β-strand	173-182	10	15
α-helix	183-187	5
β-strand	191-197	7	16
β-strand	205-210	6	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Avastin Light Chain Fab fragment mutant	B, L	protein	214	Homo sapiens	Q8TCD0 (AlphaFold model)
Avastin Heavy Chain Fab fragment mutant	A, H	protein	231	Homo sapiens	P0DOX5 (AlphaFold model)
Vascular endothelial growth factor A	C, G	protein	102	Homo sapiens	P15692 (AlphaFold model)

Sequence of entity 1 (B, L), FASTA

>6BFT_1 Avastin Light Chain Fab fragment mutant (chains B, L)
DIQMTQSPSSLSASVGDRVTITCSASQDISNYLNWYQQKPGKAPKVLIYFTDDLHSGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQQYSTVPWTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (A, H), FASTA

>6BFT_2 Avastin Heavy Chain Fab fragment mutant (chains A, H)
EVQLVESGGGLVQPGGSLRLSCAASGYDFDNYGMNWVRQAPGKGLEWVGWINTYTGEPTY
AADFKRRFTFSLDTSKSTAYLQMNSLRAEDTAVYYCAKYPHYYGSSHWYFDVWGQGTLVT
VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Sequence of entity 3 (C, G), FASTA

>6BFT_3 Vascular endothelial growth factor A (chains C, G)
GPNHHEVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLE
CVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPKKD

Primary citation

Stable human IgG antibody therapeutics with native framework structure. Christie, M., Rouet, R., Nevoltris, D. et al. To be published.

Other PDB entries of the same protein (UniProt Q8TCD0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4NWU 1.6 Å, Crystal structure of APE1551, an anti-human NGF Fab with a nine amino acid insertion in…
6ARP 1.7 Å, Structure of a mutant Cetuximab Fab fragment
6DC4 1.7 Å, RSV-neutralizing human antibody AM22
4NWT 1.75 Å, Crystal structure of the anti-human NGF Fab APE1531
6UC5 1.75 Å, Fab397 in complex with NPNA peptide
3MNZ 1.8 Å, Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment with a gp41…
4NUJ 1.83 Å, Crystal structure of HIV-1 broadly neutralizing antibody PGT152
4NUG 1.86 Å, Crystal structure of HIV-1 broadly neutralizing antibody PGT151
5VKK 2.01 Å, Crystal structure of Fab fragment of anti-CD22 Epratuzumab
3PGF 2.1 Å, Crystal structure of maltose bound MBP with a conformationally specific synthetic…
3MNW 2.2 Å, Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment with a gp41…
6E4X 2.25 Å, Human antibody S5V2-29 in complex with influenza hemagglutinin A/Texas/50/2012 (H3N2)

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