4MLP | pdb_00004mlp

Mammalian cryptochrome in complex with a small molecule competitor of its ubiquitin ligase

PDB DOI: https://doi.org/10.2210/pdb4MLP/pdb

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

Deposited: 2013-09-06 Released: 2013-10-16
Deposition Author(s): Nangle, S., Xing, W., Zheng, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.217 (Depositor), 0.205 (DCC)
R-Value Work:
0.179 (Depositor), 0.186 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of mammalian cryptochrome in complex with a small molecule competitor of its ubiquitin ligase.

Nangle, S., Xing, W., Zheng, N.

(2013) Cell Res 23: 1417-1419

PubMed: 24080726 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/cr.2013.136
Primary Citation Related Structures:
4MLP

Organizational Affiliation

Department of Pharmacology, University of Washington, Seattle, WA 98195, USA.

Macromolecule Content

Total Structure Weight: 236.35 kDa
Atom Count: 17,726
Modeled Residue Count: 1,968
Deposited Residue Count: 2,048
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cryptochrome-2	A [auth C], B [auth A], C [auth B], D	512	Mus musculus	Mutation(s): 0 Gene Names: Cry2, Kiaa0658
UniProt
Find proteins for Q9R194 (Mus musculus) Explore Q9R194 Go to UniProtKB: Q9R194
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9R194
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2CX Query on 2CX Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain H [auth D] SDF format, chain E [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth D] MOL2 format, chain E [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth D] mmCIF format, chain E [auth C]	E [auth C], F [auth A], G [auth B], H [auth D]	N-[(2S)-3-(9H-carbazol-9-yl)-2-hydroxypropyl]-N-(furan-2-ylmethyl)methanesulfonamide C₂₁ H₂₂ N₂ O₄ S OQAFDLPAPSSOHY-MRXNPFEDSA-N		Interactions Focus chain E [auth C] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth D] Interactions & Density Focus chain E [auth C] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.217 (Depositor), 0.205 (DCC)
R-Value Work: 0.179 (Depositor), 0.186 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.21	α = 89.94
b = 93.651	β = 90.09
c = 141.179	γ = 90.25

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-10-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-10-16
Type: Initial release
Version 1.1: 2013-12-18
Changes: Database references
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.