6MY5: Anti-VEGF-A Fab fragment bH1 heavy chain

Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98F,HC-G99M,LC-S30bR]. Determined by X-ray diffraction at 1.73 Å resolution. Released 31 Jul 2019.

Method: X-ray diffraction
Resolution: 1.73 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,694
Mol. weight: 99.18 kDa
Released: 31 Jul 2019

Explore 6MY5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6MY5 contains 34 α-helices and 90 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: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	13
β-strand	11-12	2	14
β-strand	18-25	8	13
α-helix	29-31	3
β-strand	34-39	6	15
β-strand	45-52	8	15
β-strand	56-59	4	15
α-helix	61-63	3
β-strand	67-72	6	13
β-strand	77-82	6	13
α-helix	84-86	3
β-strand	88-94	7	15
β-strand	102-103	2	15
β-strand	107-109	3	15
β-strand	110-111	2	14
α-helix	115-116	2
β-strand	117	1	16
α-helix	118-119	2
β-strand	120-124	5	17
β-strand	135-145	11	17
β-strand	146	1	16
β-strand	151-154	4	18
α-helix	155-157	3
β-strand	159	1	18
β-strand	163-165	3	17
α-helix	166-168	3
β-strand	169-170	2	17
β-strand	176-185	10	17
α-helix	186-188	3
β-strand	195-200	6	18
α-helix	201-203	3
β-strand	205-210	6	18

Chain B: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	19
β-strand	10-13	4	20
β-strand	19-25	7	19
β-strand	34-38	5	20
β-strand	45-49	5	20
β-strand	53-54	2	20
α-helix	55	1
β-strand	62-67	6	19
β-strand	70-75	6	19
α-helix	80-82	3
β-strand	84-90	7	20
β-strand	97-98	2	20
β-strand	102-106	5	20
β-strand	111	1	21
α-helix	112-113	2
β-strand	114-118	5	22
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	22
β-strand	140	1	21
β-strand	145-150	6	23
β-strand	153-154	2	23
α-helix	155	1
β-strand	159-163	5	22
α-helix	164-167	4
β-strand	173-182	10	22
α-helix	183-188	6
β-strand	191-197	7	23
β-strand	205-210	6	23

Chain H: 9 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	3
β-strand	45-52	8	3
β-strand	56-59	4	3
α-helix	61-63	3
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-94	7	3
β-strand	102-103	2	3
β-strand	107-109	3	3
β-strand	110-111	2	2
α-helix	115-116	2
β-strand	117	1	4
α-helix	118-119	2
β-strand	120-124	5	5
β-strand	132	1	6
β-strand	135	1	6
β-strand	136-145	10	5
β-strand	146	1	4
β-strand	151-154	4	7
α-helix	155-157	3
β-strand	159	1	7
β-strand	163-165	3	5
α-helix	166-168	3
β-strand	169-170	2	5
β-strand	176-184	9	5
α-helix	186-188	3
β-strand	195-200	6	7
α-helix	201-203	3
β-strand	205-210	6	7

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	8
β-strand	10-14	5	9
β-strand	19-25	7	8
β-strand	34-38	5	9
β-strand	45-49	5	9
β-strand	53-54	2	9
α-helix	55	1
β-strand	62-67	6	8
β-strand	70-75	6	8
α-helix	80-82	3
β-strand	84-90	7	9
β-strand	97-98	2	9
β-strand	102-107	6	9
β-strand	111	1	10
α-helix	112-113	2
β-strand	114-118	5	11
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	11
β-strand	140	1	10
β-strand	145-150	6	12
β-strand	153-154	2	12
α-helix	155	1
β-strand	159-163	5	11
α-helix	164-167	4
β-strand	173-182	10	11
α-helix	183-187	5
β-strand	191-197	7	12
β-strand	205-210	6	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
anti-VEGF-A Fab fragment bH1 heavy chain	A, H	protein	236	Homo sapiens	V9HW68 (AlphaFold model)
anti-VEGF-A Fab fragment bH1 light chain	B, L	protein	218	Homo sapiens	Q7Z3Y4 (AlphaFold model)

Sequence of entity 1 (A, H), FASTA

>6MY5_1 anti-VEGF-A Fab fragment bH1 heavy chain (chains A, H)
EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTWIHWVRQAPGKGLEWVARIYPTNGYTRY
ADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRWGGFMFYAMDYWGQGTLVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTGHHHHHHHHG

Sequence of entity 2 (B, L), FASTA

>6MY5_2 anti-VEGF-A Fab fragment bH1 light chain (chains B, L)
DIQMTQSPSSLSASVGDRVTITCRASQDIPRRISGYVAWYQQKPGKAPKLLIYWGSYLYS
GVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIKRTVAAPSVF
IFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS
STLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Primary citation

Binding symmetry and surface flexibility mediate antibody self-association. Schrag, J.D., Picard, M.E., Gaudreault, F. et al. MAbs (2019) 11:1300-1318. DOI 10.1080/19420862.2019.1632114 · PubMed

Other PDB entries of the same protein (UniProt V9HW68 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6MY4 1.69 Å, Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98M,HC-G99M,LC-S30bR]
6MXS 1.95 Å, Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98F,HC-G99M]
6MXR 2.04 Å, Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98M,HC-G99M]
7CZW 2.8 Å, S protein of SARS-CoV-2 in complex bound with P5A-2G7
7CZZ 3.2 Å, S protein of SARS-CoV-2 in complex bound with P5A-2F11_3B
7D03 3.2 Å, S protein of SARS-CoV-2 in complex bound with FabP5A-2G7
7CZY 3.3 Å, S protein of SARS-CoV-2 in complex bound with P5A-2F11_2B
6MHG 3.57 Å, Cryo-EM structure of the circumsporozoite protein of Plasmodium falciparum with a…
6U1N 4.0 Å, GPCR-Beta arrestin structure in lipid bilayer

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