4ZTE | pdb_00004zte

Crystal structure of human E-Cadherin (residues 3-213) in complex with a peptidomimetic inhibitor

PDB DOI: https://doi.org/10.2210/pdb4ZTE/pdb

Classification: CELL ADHESION
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-05-14 Released: 2016-06-01
Deposition Author(s): Nardone, V., Lucarelli, A.P., Dalle Vedove, A., Parisini, E.
Funding Organization(s): European Union

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free:
0.230 (Depositor), 0.235 (DCC)
R-Value Work:
0.185 (Depositor), 0.194 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

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., Fanelli, R., Tomassetti, A., Belvisi, L., Civera, M., Parisini, E.

(2016) J Med Chem 59: 5089-5094

PubMed: 27120112 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.5b01487
Primary Citation Related Structures:
4ZT1, 4ZTE

PubMed Abstract:
Cadherins are transmembrane cell adhesion proteins whose aberrant expression often correlates with cancer development and proliferation. We report the crystal structure of an E-cadherin extracellular fragment in complex with a peptidomimetic compound that was previously shown to partially inhibit cadherin homophilic adhesion. The structure reveals an unexpected binding mode and allows the identification of a druggable cadherin interface, thus paving the way to a future structure-guided design of cell adhesion inhibitors against cadherin-expressing solid tumors.

Organizational Affiliation

Center for Nano Science and Technology @PoliMi, Istituto Italiano di Tecnologia , Via G. Pascoli 70/3, 20133 Milano, Italy.

Macromolecule Content

Total Structure Weight: 47.09 kDa
Atom Count: 3,513
Modeled Residue Count: 420
Deposited Residue Count: 422
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cadherin-1	A, B	211	Homo sapiens	Mutation(s): 0 Gene Names: CDH1, CDHE, UVO
UniProt & NIH Common Fund Data Resources
Find proteins for P12830 (Homo sapiens) Explore P12830 Go to UniProtKB: P12830
PHAROS: P12830 GTEx: ENSG00000039068
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12830
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4RL Query on 4RL Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A]	F [auth A], J [auth B]	N-{[(2S,5S)-1-benzyl-5-(2-{[(2S,3S)-1-(tert-butylamino)-3-methyl-1-oxopentan-2-yl]amino}-2-oxoethyl)-3,6-dioxopiperazin-2-yl]methyl}-L-alpha-asparagine C₂₈ H₄₂ N₆ O₇ QOSIRQNYWJNZFB-WGLQCKHLSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] G [auth B] H [auth B] C [auth A], D [auth A], E [auth A], G [auth B], H [auth B], I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free: 0.230 (Depositor), 0.235 (DCC)
R-Value Work: 0.185 (Depositor), 0.194 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.579	α = 90
b = 76.835	β = 111.14
c = 72.772	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
MOLREP	phasing
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-06-01

Deposition Author(s):

Funding Organization	Location	Grant Number
European Union		FP7-PEOPLE-2010-RG (N. 268231)

Revision History (Full details and data files)

Version 1.0: 2016-06-01
Type: Initial release
Version 1.1: 2016-06-08
Changes: Database references
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description