2YDC | pdb_00002ydc

Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, soaked with GTP

PDB DOI: https://doi.org/10.2210/pdb2YDC/pdb

Classification: HYDROLASE
Organism(s): Mus musculus
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2011-03-18 Released: 2012-03-28
Deposition Author(s): Myllykoski, M., Kursula, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.248 (Depositor), 0.235 (DCC)
R-Value Work:
0.202 (Depositor), 0.195 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Structural Characterization of Mouse Cnpase Complexed with Active-Site Ligands

Myllykoski, M., Kursula, P.

To be published.

Macromolecule Content

Total Structure Weight: 24.74 kDa
Atom Count: 1,794
Modeled Residue Count: 217
Deposited Residue Count: 221
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2', 3'-CYCLIC NUCLEOTIDE 3'-PHOSPHODIESTERASE	A	221	Mus musculus	Mutation(s): 0 EC: 3.1.4.37
UniProt & NIH Common Fund Data Resources
Find proteins for P16330 (Mus musculus) Explore P16330 Go to UniProtKB: P16330
IMPC: MGI:88437
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P16330
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.248 (Depositor), 0.235 (DCC)
R-Value Work: 0.202 (Depositor), 0.195 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.89	α = 90
b = 46.43	β = 90
c = 106.49	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-03-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-03-28
Type: Initial release
Version 1.1: 2012-06-27
Changes: Other
Version 1.2: 2018-01-17
Changes: Data collection
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, 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.