6WTC | pdb_00006wtc

Crystal Structure of the Second Form of the Co-factor Complex of NSP7 and the C-terminal Domain of NSP8 from SARS CoV-2

PDB DOI: https://doi.org/10.2210/pdb6WTC/pdb

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-05-02 Released: 2020-05-13
Deposition Author(s): Wilamowski, M., Kim, Y., Jedrzejczak, R., Maltseva, N., Endres, M., Godzik, A., Michalska, K., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.214 (Depositor), 0.210 (DCC)
R-Value Work:
0.187 (Depositor), 0.190 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of the Second Form of the Co-factor Complex of NSP7 and the C-terminal Domain of NSP8 from SARS CoV-2

Wilamowski, M., Kim, Y., Jedrzejczak, R., Maltseva, N., Endres, M., Godzik, A., Michalska, K., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 46.19 kDa
Atom Count: 3,023
Modeled Residue Count: 378
Deposited Residue Count: 416
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 7	A, C	86	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 8	B, D	122	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain F [auth C] MOL2 format, chain E [auth B] MOL2 format, chain F [auth C] mmCIF format, chain E [auth B] mmCIF format, chain F [auth C]	E [auth B], F [auth C]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain E [auth B] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.214 (Depositor), 0.210 (DCC)
R-Value Work: 0.187 (Depositor), 0.190 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.59	α = 90
b = 120.081	β = 91.953
c = 43.309	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-05-13

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2020-05-13
Type: Initial release
Version 1.1: 2021-01-27
Changes: Structure summary
Version 1.2: 2023-10-18
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-10-23
Changes: Structure summary