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), 0.248 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5B21

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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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.248 (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

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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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.