6CXY | pdb_00006cxy

Crystal Structure of Human E-cadherin bound by mouse monoclonal antibody Fab mAb-1_19A11

PDB DOI: https://doi.org/10.2210/pdb6CXY/pdb

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

Deposited: 2018-04-04 Released: 2019-04-10
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.197 (Depositor), 0.200 (DCC)
R-Value Work:
0.163 (Depositor), 0.160 (DCC)
R-Value Observed:
0.164 (Depositor)

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of Human E-cadherin bound by mouse monoclonal antibody Fab mAb-1_19A11

Dranow, D.M., Phan, J.N., Maker, A.Y., Schecterson, L.C., Mangio, R.S., Gumbiner, B.M., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 73.73 kDa
Atom Count: 5,633
Modelled Residue Count: 640
Deposited Residue Count: 664
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cadherin-1	A [auth C]	217	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P12830
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain	B [auth H]	227	Mus musculus	Mutation(s): 0 Gene Names: Ighg1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Light Chain	C [auth L]	220	Mus musculus	Mutation(s): 0 Gene Names: LC
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain I [auth C] MOL2 format, chain I [auth C] mmCIF format, chain I [auth C]	I [auth C]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Interactions & Density Focus chain I [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth C] SDF format, chain H [auth C] SDF format, chain J [auth H] SDF format, chain K [auth H] SDF format, chain L [auth H] SDF format, chain M [auth H] SDF format, chain N [auth H] SDF format, chain O [auth H] SDF format, chain P [auth H] SDF format, chain Q [auth H] SDF format, chain R [auth L] SDF format, chain S [auth L] SDF format, chain T [auth L] SDF format, chain U [auth L] SDF format, chain V [auth L] SDF format, chain W [auth L] SDF format, chain X [auth L] SDF format, chain Y [auth L] MOL2 format, chain G [auth C] MOL2 format, chain H [auth C] MOL2 format, chain J [auth H] MOL2 format, chain K [auth H] MOL2 format, chain L [auth H] MOL2 format, chain M [auth H] MOL2 format, chain N [auth H] MOL2 format, chain O [auth H] MOL2 format, chain P [auth H] MOL2 format, chain Q [auth H] MOL2 format, chain R [auth L] MOL2 format, chain S [auth L] MOL2 format, chain T [auth L] MOL2 format, chain U [auth L] MOL2 format, chain V [auth L] MOL2 format, chain W [auth L] MOL2 format, chain X [auth L] MOL2 format, chain Y [auth L] mmCIF format, chain G [auth C] mmCIF format, chain H [auth C] mmCIF format, chain J [auth H] mmCIF format, chain K [auth H] mmCIF format, chain L [auth H] mmCIF format, chain M [auth H] mmCIF format, chain N [auth H] mmCIF format, chain O [auth H] mmCIF format, chain P [auth H] mmCIF format, chain Q [auth H] mmCIF format, chain R [auth L] mmCIF format, chain S [auth L] mmCIF format, chain T [auth L] mmCIF format, chain U [auth L] mmCIF format, chain V [auth L] mmCIF format, chain W [auth L] mmCIF format, chain X [auth L] mmCIF format, chain Y [auth L]	G [auth C] H [auth C] J [auth H] K [auth H] L [auth H] G [auth C], H [auth C], J [auth H], K [auth H], L [auth H], M [auth H], N [auth H], O [auth H], P [auth H], Q [auth H], R [auth L], S [auth L], T [auth L], U [auth L], V [auth L], W [auth L], X [auth L], Y [auth L]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth C] Focus chain H [auth C] Focus chain J [auth H] Focus chain K [auth H] Focus chain L [auth H] Focus chain M [auth H] Focus chain N [auth H] Focus chain O [auth H] Focus chain P [auth H] Focus chain Q [auth H] Focus chain R [auth L] Focus chain S [auth L] Focus chain T [auth L] Focus chain U [auth L] Focus chain V [auth L] Focus chain W [auth L] Focus chain X [auth L] Focus chain Y [auth L] Interactions & Density Focus chain G [auth C] Focus chain H [auth C] Focus chain J [auth H] Focus chain K [auth H] Focus chain L [auth H] Focus chain M [auth H] Focus chain N [auth H] Focus chain O [auth H] Focus chain P [auth H] Focus chain Q [auth H] Focus chain R [auth L] Focus chain S [auth L] Focus chain T [auth L] Focus chain U [auth L] Focus chain V [auth L] Focus chain W [auth L] Focus chain X [auth L] Focus chain Y [auth L]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth C] SDF format, chain E [auth C] SDF format, chain F [auth C] MOL2 format, chain D [auth C] MOL2 format, chain E [auth C] MOL2 format, chain F [auth C] mmCIF format, chain D [auth C] mmCIF format, chain E [auth C] mmCIF format, chain F [auth C]	D [auth C], E [auth C], F [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth C] Focus chain E [auth C] Focus chain F [auth C] Interactions & Density Focus chain D [auth C] Focus chain E [auth C] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.197 (Depositor), 0.200 (DCC)
R-Value Work: 0.163 (Depositor), 0.160 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.68	α = 90
b = 77.47	β = 92.91
c = 110.94	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2019-04-10

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2019-04-10
Type: Initial release
Version 1.1: 2020-01-15
Changes: Data collection
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-10-09
Changes: Structure summary