5X6Z | pdb_00005x6z

Crystal structure of Rice Dwarf Virus P5 in complex with GTP and GDP

PDB DOI: https://doi.org/10.2210/pdb5X6Z/pdb

Classification: TRANSFERASE
Organism(s): Rice dwarf virus (isolate O)
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2017-02-23 Released: 2018-02-28
Deposition Author(s): Nakamichi, Y., Higashiura, A., Nakagawa, A.
Funding Organization(s): JSPS

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.235 (Depositor), 0.230 (DCC)
R-Value Work:
0.184 (Depositor), 0.180 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of the capping enzyme P5 from Rice Dwarf Virus

Nakamichi, Y., Higashiura, A., Narita, H., Hagiwara, K., Uehara-Ichiki, T., Omura, T., Nakagawa, A.

To be published.

Macromolecule Content

Total Structure Weight: 367.08 kDa
Atom Count: 26,421
Modeled Residue Count: 3,128
Deposited Residue Count: 3,216
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mRNA capping enzyme P5	A [auth C], B [auth A], C [auth D], D [auth B]	804	Rice dwarf virus (isolate O)	Mutation(s): 0 EC: 2.7.7.50
UniProt
Find proteins for P14583 (Rice dwarf virus (isolate Akita)) Explore P14583 Go to UniProtKB: P14583
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14583
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download Ideal Coordinates CCD File SDF format, chain E [auth C] SDF format, chain G [auth A] SDF format, chain I [auth D] SDF format, chain K [auth B] MOL2 format, chain E [auth C] MOL2 format, chain G [auth A] MOL2 format, chain I [auth D] MOL2 format, chain K [auth B] mmCIF format, chain E [auth C] mmCIF format, chain G [auth A] mmCIF format, chain I [auth D] mmCIF format, chain K [auth B]	E [auth C], G [auth A], I [auth D], K [auth B]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain E [auth C] Focus chain G [auth A] Focus chain I [auth D] Focus chain K [auth B] Interactions & Density Focus chain E [auth C] Focus chain G [auth A] Focus chain I [auth D] Focus chain K [auth B]
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain H [auth A] SDF format, chain J [auth D] SDF format, chain L [auth B] MOL2 format, chain F [auth C] MOL2 format, chain H [auth A] MOL2 format, chain J [auth D] MOL2 format, chain L [auth B] mmCIF format, chain F [auth C] mmCIF format, chain H [auth A] mmCIF format, chain J [auth D] mmCIF format, chain L [auth B]	F [auth C], H [auth A], J [auth D], L [auth B]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain F [auth C] Focus chain H [auth A] Focus chain J [auth D] Focus chain L [auth B] Interactions & Density Focus chain F [auth C] Focus chain H [auth A] Focus chain J [auth D] Focus chain L [auth B]