7XXK

Crystal structure of SARS-CoV-2 N-CTD in complex with GMP

PDB DOI: https://doi.org/10.2210/pdb7XXK/pdb

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-05-30 Released: 2022-06-29
Deposition Author(s): Zhou, R.J., Ni, X.C., Lei, J.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.232
R-Value Work: 0.178
R-Value Observed: 0.181

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 SARS-CoV-2 N-CTD in complex with GMP

Zhou, R.J., Ni, X.C., Lei, J.

To be published.

Macromolecule Content

Total Structure Weight: 82.69 kDa
Atom Count: 6,167
Modelled Residue Count: 648
Deposited Residue Count: 720
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoprotein	A, B, C, D, E A, B, C, D, E, F	120	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for P0DTC9 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC9 Go to UniProtKB: P0DTC9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTC9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5GP (Subject of Investigation/LOI) Query on 5GP Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain S [auth C] SDF format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain S [auth C] MOL2 format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain S [auth C] mmCIF format, chain H [auth A]	H [auth A], I [auth A], S [auth C]	GUANOSINE-5'-MONOPHOSPHATE C₁₀ H₁₄ N₅ O₈ P RQFCJASXJCIDSX-UUOKFMHZSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain S [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain S [auth C]
GMP (Subject of Investigation/LOI) Query on GMP Download Ideal Coordinates CCD File SDF format, chain FA [auth F] MOL2 format, chain FA [auth F] mmCIF format, chain FA [auth F]	FA [auth F]	GUANOSINE C₁₀ H₁₃ N₅ O₅ NYHBQMYGNKIUIF-UUOKFMHZSA-N		Interactions Focus chain FA [auth F] Interactions & Density Focus chain FA [auth F]
GUN (Subject of Investigation/LOI) Query on GUN Download Ideal Coordinates CCD File SDF format, chain R [auth C] MOL2 format, chain R [auth C] mmCIF format, chain R [auth C]	R [auth C]	GUANINE C₅ H₅ N₅ O UYTPUPDQBNUYGX-UHFFFAOYSA-N		Interactions Focus chain R [auth C] Interactions & Density Focus chain R [auth C]
SCN Query on SCN Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
K Query on K Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain GA [auth F] SDF format, chain N [auth B] SDF format, chain T [auth C] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain GA [auth F] MOL2 format, chain N [auth B] MOL2 format, chain T [auth C] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain GA [auth F] mmCIF format, chain N [auth B] mmCIF format, chain T [auth C]	AA [auth D] BA [auth D] GA [auth F] J [auth A] K [auth A] AA [auth D], BA [auth D], GA [auth F], J [auth A], K [auth A], L [auth A], M [auth A], N [auth B], T [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain GA [auth F] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain T [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain GA [auth F] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain T [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain EA [auth E] SDF format, chain HA [auth F] SDF format, chain O [auth B] SDF format, chain Q [auth B] SDF format, chain V [auth C] SDF format, chain CA [auth D] SDF format, chain DA [auth E] SDF format, chain IA [auth F] SDF format, chain P [auth B] SDF format, chain U [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] MOL2 format, chain EA [auth E] MOL2 format, chain HA [auth F] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain V [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth E] MOL2 format, chain IA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain U [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] mmCIF format, chain EA [auth E] mmCIF format, chain HA [auth F] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain V [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth E] mmCIF format, chain IA [auth F] mmCIF format, chain P [auth B] mmCIF format, chain U [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C]	CA [auth D] DA [auth E] EA [auth E] HA [auth F] IA [auth F] CA [auth D], DA [auth E], EA [auth E], HA [auth F], IA [auth F], O [auth B], P [auth B], Q [auth B], U [auth C], V [auth C], W [auth C], X [auth C], Y [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CA [auth D] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain CA [auth D] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain JA [auth F] MOL2 format, chain Z [auth C] MOL2 format, chain JA [auth F] mmCIF format, chain Z [auth C] mmCIF format, chain JA [auth F]	JA [auth F], Z [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain JA [auth F] Focus chain Z [auth C] Interactions & Density Focus chain JA [auth F] Focus chain Z [auth C]