9ERT | pdb_00009ert

Mouse CNPase catalytic domain with nano body 5E

PDB DOI: https://doi.org/10.2210/pdb9ERT/pdb

Classification: PROTEIN BINDING
Organism(s): Mus musculus, Vicugna pacos
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-03-25 Released: 2024-12-11
Deposition Author(s): Markusson, S., Raasakka, A., Opazo, F., Kursula, P.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.323 (Depositor), 0.323 (DCC)
R-Value Work:
0.289 (Depositor), 0.289 (DCC)
R-Value Observed:
0.293 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

Mouse CNPase catalytic domain with nano body 5E

Markusson, S., Raasakka, A., Opazo, F., Kursula, P.

To be published.

Macromolecule Content

Total Structure Weight: 38.51 kDa
Atom Count: 2,641
Modeled Residue Count: 342
Deposited Residue Count: 352
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2',3'-cyclic-nucleotide 3'-phosphodiesterase	A	220	Mus musculus	Mutation(s): 0 Gene Names: Cnp, Cnp1 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

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Chains: B	B	132	Vicugna pacos	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.323 (Depositor), 0.323 (DCC)
R-Value Work: 0.289 (Depositor), 0.289 (DCC)
R-Value Observed: 0.293 (Depositor)

Diffraction Data:

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.832	α = 90
b = 110.832	β = 90
c = 83.281	γ = 120

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-12-11

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-12-11
Type: Initial release

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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.