8CTM | pdb_00008ctm

Crystal structure of the nucleoside hydrolase from Leishmania donovani.

PDB DOI: https://doi.org/10.2210/pdb8CTM/pdb

Classification: HYDROLASE
Organism(s): Leishmania donovani
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-05-16 Released: 2023-06-28
Deposition Author(s): Chen, Y., Tolbert, W.D., Pazgier, M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free:
0.207 (Depositor), 0.204 (DCC)
R-Value Work:
0.174 (Depositor), 0.175 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8CTM

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

Literature

Crystal structure of the nucleoside hydrolase from Leishmania donovani.

Chen, Y., Tolbert, W.D., Pazgier, M.

To be published.

Macromolecule Content

Total Structure Weight: 138.55 kDa
Atom Count: 10,338
Modeled Residue Count: 1,223
Deposited Residue Count: 1,256
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inosine-uridine preferring nucleoside hydrolase	A, B, C, D	314	Leishmania donovani	Mutation(s): 0 Gene Names: iunh, CGC20_39000, CGC21_5445, LdCL_180021000, LDHU3_18.2000 EC: 3.2.2.1
UniProt
Find proteins for Q8WQX2 (Leishmania donovani) Explore Q8WQX2 Go to UniProtKB: Q8WQX2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8WQX2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain F [auth A] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain F [auth A] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain F [auth A]	F [auth A], R [auth D], S [auth D]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain F [auth A] Focus chain R [auth D] Focus chain S [auth D]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain H [auth A]	H [auth A], M [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Interactions & Density Focus chain H [auth A] Focus chain M [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain N [auth C] SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain N [auth C] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain N [auth C] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B], N [auth C], Q [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain Q [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain T [auth D] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain T [auth D] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A], J [auth B], O [auth C], P [auth C], T [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain T [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B]	K [auth B], L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain K [auth B] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.207 (Depositor), 0.204 (DCC)
R-Value Work: 0.174 (Depositor), 0.175 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.221	α = 90
b = 79.111	β = 90.77
c = 107.621	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-06-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-06-28
Type: Initial release
Version 1.1: 2023-10-25
Changes: Data collection, Refinement description

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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.