5ISY

Crystal structure of Nudix family protein with NAD

PDB DOI: https://doi.org/10.2210/pdb5ISY/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2016-03-15 Released: 2016-09-14
Deposition Author(s): Zhang, D., Guan, Z., Zou, T., Yin, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.244
R-Value Work: 0.182
R-Value Observed: 0.185

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural basis of prokaryotic NAD-RNA decapping by NudC

Zhang, D., Liu, Y., Wang, Q., Guan, Z., Wang, J., Liu, J., Zou, T., Yin, P.

(2016) Cell Res 26: 1062-1066

PubMed: 27561816 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/cr.2016.98
Primary Citation of Related Structures:
5ISY

Organizational Affiliation

National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.

Macromolecule Content

Total Structure Weight: 61.32 kDa
Atom Count: 4,338
Modelled Residue Count: 502
Deposited Residue Count: 518
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH pyrophosphatase	A, B [auth C]	259	Escherichia coli K-12	Mutation(s): 1 Gene Names: nudC, yjaD, b3996, JW5548 EC: 3.6.1.22
UniProt
Find proteins for P32664 (Escherichia coli (strain K12)) Explore P32664 Go to UniProtKB: P32664
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P32664
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth C] MOL2 format, chain D [auth A] MOL2 format, chain F [auth C]	D [auth A], F [auth C]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain D [auth A] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain F [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth C] MOL2 format, chain C [auth A] MOL2 format, chain E [auth C]	C [auth A], E [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth C] Interactions & Density Focus chain C [auth A] Focus chain E [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.244
R-Value Work: 0.182
R-Value Observed: 0.185
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.411	α = 90
b = 98.702	β = 90
c = 113.739	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data collection
HKL-3000	data processing
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-09-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-09-14
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

5ISY

Crystal structure of Nudix family protein with NAD

Structural basis of prokaryotic NAD-RNA decapping by NudC

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)