6PWY | pdb_00006pwy

Structure of C. elegans ZK177.8, SAMHD1 ortholog

PDB DOI: https://doi.org/10.2210/pdb6PWY/pdb

Classification: HYDROLASE
Organism(s): Caenorhabditis elegans
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2019-07-24 Released: 2020-07-29
Deposition Author(s): Lim, C.S., Maehigashi, T., Wade, L.R., Bowen, N., Knecht, K., Xiong, Y., Kim, B.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free:
0.209 (Depositor), 0.212 (DCC)
R-Value Work:
0.182 (Depositor), 0.188 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

ZK177.8 of Caenorhabditis elegans: Aicardi-Goutieres Syndrome SAMHD1 Ortholog

Maehigashi, T., Lim, C., Wade, L.R., Bowen, N., Knecht, K., Schinazi, R.F., Xiong, Y., Kim, B.

To be published.

Macromolecule Content

Total Structure Weight: 246.1 kDa
Atom Count: 18,205
Modeled Residue Count: 2,033
Deposited Residue Count: 2,104
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ZK177.8	A, B, C [auth D], D [auth C]	526	Caenorhabditis elegans	Mutation(s): 2 Gene Names: ZK177.8 EC: 3.1.5
UniProt
Find proteins for Q09374 (Caenorhabditis elegans) Explore Q09374 Go to UniProtKB: Q09374
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q09374
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP (Subject of Investigation/LOI) Query on GTP Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain W [auth C] SDF format, chain T [auth D] SDF format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain W [auth C] MOL2 format, chain T [auth D] MOL2 format, chain F [auth A] mmCIF format, chain M [auth B] mmCIF format, chain W [auth C] mmCIF format, chain T [auth D] mmCIF format, chain F [auth A]	F [auth A], M [auth B], T [auth D], W [auth C]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain F [auth A] Focus chain M [auth B] Focus chain T [auth D] Focus chain W [auth C] Interactions & Density Focus chain F [auth A] Focus chain M [auth B] Focus chain T [auth D] Focus chain W [auth C]
DTP (Subject of Investigation/LOI) Query on DTP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain N [auth B] SDF format, chain S [auth D] SDF format, chain U [auth D] SDF format, chain V [auth C] SDF format, chain X [auth C] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth B] MOL2 format, chain S [auth D] MOL2 format, chain U [auth D] MOL2 format, chain V [auth C] MOL2 format, chain X [auth C] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth B] mmCIF format, chain S [auth D] mmCIF format, chain U [auth D] mmCIF format, chain V [auth C] mmCIF format, chain X [auth C]	E [auth A] G [auth A] L [auth B] N [auth B] S [auth D] E [auth A], G [auth A], L [auth B], N [auth B], S [auth D], U [auth D], V [auth C], X [auth C]	2'-DEOXYADENOSINE 5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₂ P₃ SUYVUBYJARFZHO-RRKCRQDMSA-N		Interactions Focus chain E [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain N [auth B] Focus chain S [auth D] Focus chain U [auth D] Focus chain V [auth C] Focus chain X [auth C] Interactions & Density Focus chain E [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain N [auth B] Focus chain S [auth D] Focus chain U [auth D] Focus chain V [auth C] Focus chain X [auth C]
SIN Query on SIN Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain P [auth B] SDF format, chain Y [auth C] SDF format, chain Z [auth C] SDF format, chain Q [auth B] SDF format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain J [auth A]	J [auth A] K [auth A] P [auth B] Q [auth B] Y [auth C] J [auth A], K [auth A], P [auth B], Q [auth B], Y [auth C], Z [auth C]	SUCCINIC ACID C₄ H₆ O₄ KDYFGRWQOYBRFD-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain R [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain R [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain O [auth B] mmCIF format, chain R [auth D]	H [auth A], I [auth A], O [auth B], R [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain R [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain R [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free: 0.209 (Depositor), 0.212 (DCC)
R-Value Work: 0.182 (Depositor), 0.188 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.681	α = 65.58
b = 90.557	β = 65.49
c = 93.357	γ = 86.22

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
BUCCANEER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-07-29

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	AI150451
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	AI136581

Revision History (Full details and data files)

Version 1.0: 2020-07-29
Type: Initial release
Version 1.1: 2022-03-16
Changes: Author supporting evidence, Database references
Version 1.2: 2023-10-11
Changes: Data collection, Refinement description