3H95

Crystal structure of the NUDIX domain of NUDT6

PDB DOI: https://doi.org/10.2210/pdb3H95/pdb

Deposited: 2009-04-30 Released: 2009-07-07
Deposition Author(s): Tresaugues, L., Moche, M., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Karlberg, T., Kotyenova, T., Kotzch, A., Nielsen, T.K., Nyman, T., Persson, C., Sagemark, J., Schueler, H., Schutz, P., Siponen, M.I., Svensson, L., Thorsell, A.G., Van Den Berg, S., Weigelt, J., Welin, M., Wisniewska, M., Nordlund, P., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.221
R-Value Work: 0.194
R-Value Observed: 0.196

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of the NUDIX domain of NUDT6

Tresaugues, L., Moche, M., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Karlberg, T., Kotyenova, T., Kotzch, A., Nielsen, T.K., Nyman, T., Persson, C., Sagemark, J., Schueler, H., Schutz, P., Siponen, M.I., Svensson, L., Thorsell, A.G., Van Den Berg, S., Weigelt, J., Welin, M., Wisniewska, M., Nordlund, P.

To be published.

Macromolecule Content

Total Structure Weight: 23.36 kDa
Atom Count: 1,542
Modelled Residue Count: 161
Deposited Residue Count: 199
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside diphosphate-linked moiety X motif 6	A	199	Homo sapiens	Mutation(s): 0 Gene Names: FGF2AS, NUDT6 EC: 3.6.1
UniProt & NIH Common Fund Data Resources
Find proteins for P53370 (Homo sapiens) Explore P53370 Go to UniProtKB: P53370
PHAROS: P53370 GTEx: ENSG00000170917
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P53370
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FLC Query on FLC 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]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.221
R-Value Work: 0.194
R-Value Observed: 0.196
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.53	α = 90
b = 54.53	β = 90
c = 133.71	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MrBUMP	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-07-07

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2009-07-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description