6CXY: Cadherin-1

Crystal Structure of Human E-cadherin bound by mouse monoclonal antibody Fab mAb-1_19A11. Determined by X-ray diffraction at 2.2 Å resolution. Released 10 Apr 2019.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Homo sapiens, Mus musculus
Chains: 3
Atoms: 5,633
Mol. weight: 73.73 kDa
Ligands: CA
Released: 10 Apr 2019

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

Secondary structure: helices and β-sheets

6CXY contains 22 α-helices and 65 β-strands across 3 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 C: 4 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
β-strand	7-10	4	1
β-strand	19-23	5	2
α-helix	27-30	4
β-strand	34-39	6	1
β-strand	41	1	3
β-strand	45	1	3
β-strand	51-53	3	2
β-strand	59-62	4	2
β-strand	73-82	10	1
β-strand	87	1	1
β-strand	92-99	8	1
β-strand	107-108	2	4
β-strand	112-118	7	5
α-helix	121-122	2
β-strand	126-129	4	6
β-strand	132-133	2	4
β-strand	147-154	8	5
β-strand	163-165	3	6
β-strand	171-174	4	6
β-strand	186-194	9	5
α-helix	196-198	3
β-strand	202-212	11	5

Chain H: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	11-12	2	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	33-39	7	9
β-strand	46-51	6	9
β-strand	57-59	3	9
α-helix	64-66	3
β-strand	67-72	6	7
α-helix	73-75	3
β-strand	77-82	6	7
α-helix	87-89	3
β-strand	91-98	8	9
α-helix	100-102	3
β-strand	106-109	4	9
β-strand	113-115	3	9
β-strand	116-117	2	8
α-helix	121-122	2
β-strand	123	1	10
α-helix	124-125	2
β-strand	126-130	5	11
β-strand	141-151	11	11
β-strand	152	1	10
β-strand	157-160	4	12
α-helix	161-163	3
β-strand	165	1	12
β-strand	169-171	3	11
α-helix	172-174	3
β-strand	175-177	3	11
β-strand	180-190	11	11
β-strand	200-205	6	12
α-helix	206-208	3
β-strand	210-215	6	12

Chain L: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-14	5	14
β-strand	19-25	7	13
β-strand	30-31	2	15
β-strand	36-37	2	15
β-strand	39-44	6	14
β-strand	51-55	5	14
β-strand	59-60	2	14
α-helix	61	1
β-strand	68-73	6	13
β-strand	76-81	6	13
α-helix	86-88	3
β-strand	90-96	7	14
α-helix	102	1
β-strand	103-104	2	14
β-strand	108-113	6	14
β-strand	117	1	16
α-helix	118-119	2
β-strand	120-124	5	17
α-helix	125-127	3
α-helix	128-132	5
β-strand	135-145	11	17
β-strand	146	1	16
β-strand	151-156	6	18
β-strand	159-161	3	18
β-strand	165-169	5	17
α-helix	170-173	4
β-strand	179-188	10	17
α-helix	189-193	5
β-strand	197-204	8	18
β-strand	207-216	10	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cadherin-1	C	protein	217	Homo sapiens	P12830 (AlphaFold model)
Heavy chain	H	protein	227	Mus musculus
Light Chain	L	protein	220	Mus musculus

Sequence of entity 1 (C), FASTA

>6CXY_1 Cadherin-1 (chains C)
DWVIPPISCPENEKGPFPKNLVQIKSNKDKEGKVFYSITGQGADTPPVGVFIIERETGWL
KVTEPLDRERIATYTLFSHAVSSNGNAVEDPMEILITVTDQNDNKPEFTQEVFKGSVMEG
ALPGTSVMEVTATDADDDVNTYNAAIAYTILSQDPELPDKNMFTINRNTGVISVVTTGLD
RESFPTYTLVVQAADLQGEGLSTTATAVITVTDTNDN

Sequence of entity 2 (H), FASTA

>6CXY_2 Heavy chain (chains H)
QVQLKESGPGLVAPSQSLSITCTVSGFSLSRYGVHWVRQPPGKGLEWLGMMWGGGNTDYN
SALKSRLSISKDNSKSQVFLKMNSLQTDDTAMYYCASSNYVLGYAMDYWGQGTSVTVSSA
KTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDL
YTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDCHHHHHH

Sequence of entity 3 (L), FASTA

>6CXY_3 Light Chain (chains L)
DIVMTQSPSSLAMSVGQKVTMNCKSSQSLLNSSNQKNYLAWYQQKPGQSPKLLIYFTSTR
GSGVPDRFIGSGSGTDFTLTISSVEAEDLADYFCQQHYRTPHTFGGGTKVEIKRADAAPT
VSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYS
MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	3

Water and common crystallization additives (EDO, PG4) are not listed.

Primary citation

Crystal Structure of Human E-cadherin bound by mouse monoclonal antibody Fab mAb-1_19A11. Dranow, D.M., Phan, J.N., Maker, A.Y. et al. To be published.

Other PDB entries of the same protein (UniProt P12830 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2OMZ 1.6 Å, Crystal structure of InlA Y369A/hEC1 complex
2OMX 1.7 Å, Crystal structure of InlA S192N G194S+S/hEC1 complex
2OMY 1.7 Å, Crystal structure of InlA S192N/hEC1 complex
1O6S 1.8 Å, Internalin (Listeria monocytogenes) / E-Cadherin (human) Recognition Complex
2OMU 1.8 Å, Crystal structure of InlA G194S+S Y369S/hEC1 complex
3FF7 1.8 Å, Structure of NK cell receptor KLRG1 bound to E-cadherin
2OMV 1.9 Å, Crystal structure of InlA S192N Y369S/hEC1 complex
8H62 1.91 Å, Crystal structure of Internalin A from Listeria monocytogenes with human E-cadherin EC12
4ZT1 1.92 Å, Crystal structure of human E-Cadherin (residues 3-213) in x-dimer conformation
2O72 2.0 Å, Crystal Structure Analysis of human E-cadherin (1-213)
2OMT 2.0 Å, Crystal structure of InlA G194S+S/hEC1 complex
3FF8 2.0 Å, Structure of NK cell receptor KLRG1 bound to E-cadherin

Browse structure collections

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