8C0G | pdb_00008c0g

SARS-CoV nsp16-nsp10 complexed with N7-GTP

PDB DOI: https://doi.org/10.2210/pdb8C0G/pdb

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome-related coronavirus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-12-16 Released: 2023-12-27
Deposition Author(s): Ferron, F., Debarnot, C., Coutard, B., Canard, B., Marseilles Structural Genomics Program @ AFMB (MSGP)
Funding Organization(s): European Union (EU)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free:
0.263 (Depositor), 0.248 (DCC)
R-Value Work:
0.245 (Depositor), 0.230 (DCC)
R-Value Observed:
0.246 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Observation of N7-GTP in nsp16-nsp10 Sars-CoV

Ferron, F., Canard, B., Debarnot, C., Coutard, B.

To be published.

Macromolecule Content

Total Structure Weight: 46.82 kDa
Atom Count: 3,442
Modeled Residue Count: 409
Deposited Residue Count: 414
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 7	A	292	Severe acute respiratory syndrome-related coronavirus	Mutation(s): 0 Gene Names: rep, 1a-1b
UniProt
Find proteins for P0C6X7 (Severe acute respiratory syndrome coronavirus) Explore P0C6X7 Go to UniProtKB: P0C6X7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0C6X7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 7	B	122	Severe acute respiratory syndrome-related coronavirus	Mutation(s): 0 Gene Names: rep, 1a-1b
UniProt
Find proteins for P0C6X7 (Severe acute respiratory syndrome coronavirus) Explore P0C6X7 Go to UniProtKB: P0C6X7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0C6X7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SRC (Subject of Investigation/LOI) Query on SRC Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	[[(2~{R},3~{S},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1,8-dihydropurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate C₁₁ H₂₀ N₅ O₁₄ P₃ BUJQMJUTTBGELS-UHTZMRCNSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A]	C [auth A], E [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain E [auth A]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B]	G [auth B], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain G [auth B] Focus chain H [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.263 (Depositor), 0.248 (DCC)
R-Value Work: 0.245 (Depositor), 0.230 (DCC)
R-Value Observed: 0.246 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.232	α = 90
b = 185.042	β = 90
c = 128.577	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-12-27

Deposition Author(s):

Marseilles Structural Genomics Program @ AFMB (MSGP)

Funding Organization	Location	Grant Number
European Union (EU)	European Union	VIZIER integrated project (LSHG-CT-2004-511960)
European Union (EU)	European Union	European FP7 Capacities Project no 228292

Revision History (Full details and data files)

Version 1.0: 2023-12-27
Type: Initial release