5B21 | pdb_00005b21

Dimer structure of murine Nectin-1 D1

PDB DOI: https://doi.org/10.2210/pdb5B21/pdb

Classification: CELL ADHESION
Organism(s): Mus musculus
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2015-12-28 Released: 2016-12-28
Deposition Author(s): Sangawa, T., Takebe, K., Suzuki, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free:
0.258 (Depositor), 0.290 (DCC)
R-Value Work:
0.204 (Depositor), 0.250 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Dimer structure of murine Nectin-1 D1

Sangawa, T., Takebe, K., Suzuki, M.

To be published.

Macromolecule Content

Total Structure Weight: 25.38 kDa
Atom Count: 1,799
Modeled Residue Count: 228
Deposited Residue Count: 228
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
murine Nectin-1 D1	A, B	114	Mus musculus	Mutation(s): 0 Gene Names: Pvrl1, Hvec, Prr1
UniProt
Find proteins for Q9JKF6 (Mus musculus) Explore Q9JKF6 Go to UniProtKB: Q9JKF6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9JKF6
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free: 0.258 (Depositor), 0.290 (DCC)
R-Value Work: 0.204 (Depositor), 0.250 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.32	α = 90
b = 78.32	β = 90
c = 70.84	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
iMOSFLM	data scaling
MOLREP	phasing
REFMAC	refinement
Coot	model building

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2016-12-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-12-28
Type: Initial release
Version 1.1: 2020-02-26
Changes: Data collection
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-11-20
Changes: Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.