6F00 | pdb_00006f00

Crystal Structure of human tRNA dihydrouridine synthase (20) dsRBD E423A mutant

PDB DOI: https://doi.org/10.2210/pdb6F00/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2017-11-17 Released: 2018-12-12
Deposition Author(s): Charles, B.N., Djemel, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free:
0.228 (Depositor), 0.230 (DCC)
R-Value Work:
0.176 (Depositor), 0.180 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of human tRNA-dihydrouridine(20) synthase dsRBD E423A mutant

Charles, B.N., Djemel, H.

To be published.

Macromolecule Content

Total Structure Weight: 42.43 kDa
Atom Count: 2,563
Modeled Residue Count: 289
Deposited Residue Count: 360
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA-dihydrouridine(20) synthase [NAD(P)+]-like	A [auth B], B [auth A], C	120	Homo sapiens	Mutation(s): 1 Gene Names: DUS2, DUS2L EC: 1.3.1 (PDB Primary Data), 1.3.1.91 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NX74 (Homo sapiens) Explore Q9NX74 Go to UniProtKB: Q9NX74
PHAROS: Q9NX74 GTEx: ENSG00000167264
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NX74
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain E [auth B] SDF format, chain G [auth B] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain F [auth B] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain F [auth B] mmCIF format, chain D [auth B] mmCIF format, chain E [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain F [auth B]	D [auth B] E [auth B] F [auth B] G [auth B] H [auth A] D [auth B], E [auth B], F [auth B], G [auth B], H [auth A], I [auth A], J [auth A], N [auth C], O [auth C], P [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Interactions & Density Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain Q [auth C] SDF format, chain R [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C]	K [auth A], L [auth A], M [auth A], Q [auth C], R [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain Q [auth C] Focus chain R [auth C] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain Q [auth C] Focus chain R [auth C]