5WWD

Crystal structure of AtNUDX1

PDB DOI: https://doi.org/10.2210/pdb5WWD/pdb

Classification: HYDROLASE
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-12-31 Released: 2017-11-15
Deposition Author(s): Liu, J., Guan, Z., Yan, L., Zou, T., Yin, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.39 Å
R-Value Free: 0.177
R-Value Work: 0.176
R-Value Observed: 0.176

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Structural Insights into the Substrate Recognition Mechanism of Arabidopsis GPP-Bound NUDX1 for Noncanonical Monoterpene Biosynthesis.

Liu, J., Guan, Z., Liu, H., Qi, L., Zhang, D., Zou, T., Yin, P.

(2018) Mol Plant 11: 218-221

PubMed: 29066356 Search on PubMed
DOI: https://doi.org/10.1016/j.molp.2017.10.006
Primary Citation of Related Structures:
5GP0, 5WWD, 5WY6

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: 33.76 kDa
Atom Count: 2,624
Modelled Residue Count: 277
Deposited Residue Count: 298
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nudix hydrolase 1	A, B	149	Arabidopsis thaliana	Mutation(s): 0 Gene Names: NUDT1, NUDX1, At1g68760, F14K14.13 EC: 3.6.1.55 (PDB Primary Data), 3.6.1.67 (PDB Primary Data), 3.6.1.22 (PDB Primary Data)
UniProt
Find proteins for Q9CA40 (Arabidopsis thaliana) Explore Q9CA40 Go to UniProtKB: Q9CA40
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9CA40
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	C [auth A], I [auth B], J [auth B], K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
2ME Query on 2ME Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	METHOXYETHANE C₃ H₈ O XOBKSJJDNFUZPF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B]	F [auth A] G [auth A] H [auth A] L [auth B] M [auth B] F [auth A], G [auth A], H [auth A], L [auth B], M [auth B], N [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]
NH4 Query on NH4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.39 Å
R-Value Free: 0.177
R-Value Work: 0.176
R-Value Observed: 0.176
Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.522	α = 90
b = 83.181	β = 90
c = 115.224	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-11-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-11-15
Type: Initial release
Version 1.1: 2018-01-17
Changes: Database references
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description

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Deposit Data

Help and Resources

5WWD

Crystal structure of AtNUDX1

Structural Insights into the Substrate Recognition Mechanism of Arabidopsis GPP-Bound NUDX1 for Noncanonical Monoterpene Biosynthesis.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)