4ZTE: Human E-Cadherin

Crystal structure of human E-Cadherin (residues 3-213) in complex with a peptidomimetic inhibitor. Determined by X-ray diffraction at 2.13 Å resolution. Released 1 Jun 2016.

Method: X-ray diffraction
Resolution: 2.13 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,513
Mol. weight: 47.09 kDa
Ligands: CA, 4RL
Released: 1 Jun 2016

Explore 4ZTE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4ZTE contains 9 α-helices and 38 β-strands across 2 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: 4 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	7-10	4	1
β-strand	19-23	5	2
α-helix	27-29	3
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
α-helix	100	1
β-strand	107-108	2	4
β-strand	112-118	7	5
α-helix	121-122	2
β-strand	125-129	5	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 B: 5 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	7-10	4	7
β-strand	19-23	5	8
α-helix	27-29	3
β-strand	34-40	7	7
β-strand	41	1	9
β-strand	45	1	9
β-strand	51-53	3	8
β-strand	59-62	4	8
β-strand	73-82	10	7
β-strand	87	1	7
α-helix	90-91	2
β-strand	92-99	8	7
α-helix	100	1
β-strand	107-108	2	10
β-strand	112-118	7	11
α-helix	121-122	2
β-strand	126-129	4	12
β-strand	132-133	2	10
β-strand	147-154	8	11
β-strand	163-165	3	12
β-strand	171-174	4	12
β-strand	186-194	9	11
α-helix	196-198	3
β-strand	202-212	11	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cadherin-1	A, B	protein	211	Homo sapiens	P12830 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4ZTE_1 Cadherin-1 (chains A, B)
VIPPISCPENEKGPFPKNLVQIKSNKDKEGKVFYSITGQGADTPPVGVFIIERETGWLKV
TEPLDRERIATYTLFSHAVSSNGNAVEDPMEILITVTDQNDNKPEFTQEVFKGSVMEGAL
PGTSVMEVTATDADDDVNTYNAAIAYTILSQDPELPDKNMFTINRNTGVISVVTTGLDRE
SFPTYTLVVQAADLQGEGLSTTATAVITVTD

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	6
4RL	N-{[(2S,5S)-1-benzyl-5-(2-{[(2S,3S)-1-(tert-butylamino)-3-methyl-1-oxopentan-2-…	C28 H42 N6 O7	2

Primary citation

Crystal Structure of Human E-Cadherin-EC1EC2 in Complex with a Peptidomimetic Competitive Inhibitor of Cadherin Homophilic Interaction. Nardone, V., Lucarelli, A.P., Dalle Vedove, A. et al. J Med Chem (2016) 59:5089-5094. DOI 10.1021/acs.jmedchem.5b01487 · PubMed

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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