5X6Y | pdb_00005x6y

Crystal structure of Rice Dwarf Virus P5 in complex with S-adenosylmethionine

PDB DOI: https://doi.org/10.2210/pdb5X6Y/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:
0.245 (Depositor), 0.245 (DCC)
R-Value Work:
0.202 (Depositor), 0.202 (DCC)
R-Value Observed:
0.204 (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: 366.33 kDa
Atom Count: 24,230
Modeled Residue Count: 2,960
Deposited Residue Count: 3,216
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mRNA capping enzyme P5	A, B, C, D	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14583
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM Query on SAM Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C]	E [auth A], F [auth A], K [auth B], P [auth C], Q [auth C]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain Q [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain Q [auth C]
FLC Query on FLC Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain U [auth D] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain U [auth D] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain U [auth D]	J [auth A], O [auth B], U [auth D]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain J [auth A] Focus chain O [auth B] Focus chain U [auth D] Interactions & Density Focus chain J [auth A] Focus chain O [auth B] Focus chain U [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D]	G [auth A] H [auth A] I [auth A] L [auth B] M [auth B] G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], N [auth B], R [auth C], S [auth D], T [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth D] Focus chain T [auth D]