5VEB: Anti-CDH6 Fab heavy chain

Crystal structure of a Fab binding to extracellular domain 5 of Cadherin-6. Determined by X-ray diffraction at 2.34 Å resolution. Released 7 Jun 2017.

Method: X-ray diffraction
Resolution: 2.34 Å
Organism: Homo sapiens
Chains: 6
Atoms: 8,497
Mol. weight: 123.01 kDa
Ligands: A2G
Released: 7 Jun 2017

Explore 5VEB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5VEB contains 31 α-helices and 104 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: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	32	1	3
β-strand	34-39	6	2
β-strand	45-51	7	2
β-strand	58-60	3	2
β-strand	69-73	5	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-100	9	2
β-strand	104-108	5	2
β-strand	112-116	5	2
α-helix	120-121	2
β-strand	122	1	4
α-helix	123-124	2
β-strand	125-129	5	5
β-strand	137	1	5
β-strand	140-150	11	5
β-strand	151	1	4
β-strand	156-159	4	6
α-helix	160-162	3
β-strand	164	1	6
β-strand	168-170	3	5
α-helix	171-173	3
β-strand	174-175	2	5
β-strand	181-190	10	5
α-helix	191-193	3
β-strand	200-205	6	6
α-helix	206-208	3
β-strand	210-215	6	6

Chains B and L: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-13	4	2
β-strand	19-29	11	7
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-55	3	2
β-strand	62-75	14	7
α-helix	80-82	3
β-strand	84-90	7	2
β-strand	98-99	2	2
β-strand	103-107	5	2
β-strand	112	1	8
α-helix	113-114	2
β-strand	115-119	5	9
α-helix	120-122	3
α-helix	123-126	4
β-strand	130-140	11	9
β-strand	141	1	8
β-strand	146-151	6	10
β-strand	154-155	2	10
α-helix	156	1
β-strand	160-164	5	9
α-helix	165-168	4
β-strand	174-183	10	9
α-helix	184-188	5
β-strand	192-198	7	10
β-strand	206-211	6	10

Chain H: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	11
β-strand	10-12	3	12
β-strand	18-25	8	11
α-helix	29-31	3
β-strand	34-39	6	12
β-strand	45-51	7	12
β-strand	58-60	3	12
β-strand	69-73	5	11
β-strand	78-83	6	11
α-helix	88-90	3
β-strand	92-100	9	12
β-strand	104-108	5	12
β-strand	112-116	5	12
β-strand	122	1	13
α-helix	123-124	2
β-strand	125-129	5	14
β-strand	137	1	14
β-strand	140-150	11	14
β-strand	151	1	13
β-strand	156-159	4	15
α-helix	160-162	3
β-strand	164	1	15
β-strand	168-170	3	14
α-helix	171-173	3
β-strand	174-175	2	14
β-strand	181-190	10	14
α-helix	191-193	3
β-strand	199-205	7	15
α-helix	206-208	3
β-strand	210-216	7	15

Chain X: 1 helix, 9 β-strands

Element	Residues	Length	Sheet
β-strand	495-497	3	21
α-helix	500-501	2
β-strand	505-512	8	2
β-strand	524-527	4	21
β-strand	537-541	5	2
β-strand	546-551	6	2
β-strand	563-571	9	21
β-strand	573	1	3
β-strand	579-589	11	21
β-strand	609-612	4	2

Chain Y: 1 helix, 8 β-strands

Element	Residues	Length	Sheet
β-strand	493-497	5	22
α-helix	500-501	2
β-strand	505-512	8	17
β-strand	524-527	4	22
β-strand	537-541	5	17
β-strand	546-551	6	17
β-strand	563-571	9	22
β-strand	579-589	11	22
β-strand	609-612	4	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
anti-CDH6 Fab heavy chain	A	protein	225	Homo sapiens	S6B291 (AlphaFold model)
anti-CDH6 Fab light chain	B, L	protein	215	Homo sapiens	P01834 (AlphaFold model)
anti-CDH6 Fab heavy chain	H	protein	225	Homo sapiens	S6B291 (AlphaFold model)
Cadherin-6	X, Y	protein	125	Homo sapiens	P55285 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5VEB_1 anti-CDH6 Fab heavy chain (chains A)
QVQLLESGGGLVQPGGSLRLSCAASGFTFSSHGMHWVRQAPGKGLEWVSVISGSGSNTGY
ADSVXGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARQWGSYAFDSWGQGTLVTVSSAS
TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTH

Sequence of entity 2 (B, L), FASTA

>5VEB_2 anti-CDH6 Fab light chain (chains B, L)
DIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYAVSTLQSGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQQSGTFPPTTFGQGTKVEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (H), FASTA

>5VEB_3 anti-CDH6 Fab heavy chain (chains H)
QVQLLESGGGLVQPGGSLRLSCAASGFTFSSHGMHWVRQAPGKGLEWVSVISGSGSNTGY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARQWGSYAFDSWGQGTLVTVSSAS
TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTH

Sequence of entity 4 (X, Y), FASTA

>5VEB_4 Cadherin-6 (chains X, Y)
EFYETFVCEKAKADQLIQTLHAVDKDDPYSGHQFSFSLAPEAASGSNFTIQDNKDNTAGI
LTRKNGYNRHEMSTYLLPVVISDNDYPVQSSTGTVTVRVCACDHHGNMQSCHAEALIHPL
EVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
A2G	2-acetamido-2-deoxy-alpha-D-galactopyranose	C8 H15 N O6	4

Primary citation

Discovery and Optimization of HKT288, a Cadherin-6-Targeting ADC for the Treatment of Ovarian and Renal Cancers. Bialucha, C.U., Collins, S.D., Li, X. et al. Cancer Discov (2017) 7:1030-1045. DOI 10.1158/2159-8290.CD-16-1414 · PubMed

Other PDB entries of the same protein (UniProt S6B291 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4LLY 1.6 Å, Crystal structure of Pertuzumab Clambda Fab with variable and constant domain redesigns…
3MNZ 1.8 Å, Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment with a gp41…
6B9Z 1.82 Å, Trastuzumab Fab v3
4LLW 1.95 Å, Crystal structure of Pertuzumab Clambda Fab with variable domain redesign (VRD2) at 1.95A
6BAE 2.14 Å, Trastuzumab Fab v3 in complex with CQFDLSTRRLKC
3MNW 2.2 Å, Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment with a gp41…
6AZK 2.48 Å, Structure of cetuximab with aminoheptanoic acid-linked N-(3-hydroxypropyl)-L-arginine…
6AYN 2.48 Å, Structure of cetuximab with aminoheptanoic acid-linked N-(3-aminopropyl)-L-arginine…
6AZL 2.48 Å, Structure of cetuximab with aminoheptanoic acid-linked N-carboxyethylarginine meditope…
6AU5 2.48 Å, Structure of cetuximab with aminoheptanoic acid-linked n-butylarginine meditope variant
6AXP 2.48 Å, Structure of cetuximab with aminoheptanoic acid-linked n-octylarginine meditope variant
6VTU 2.61 Å, DH717.1 Fab monomer in complex with man9 glycan

Browse structure collections

About this viewer

MolViewer shows 5VEB directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.