7DOI

Structure of COVID-19 RNA-dependent RNA polymerase bound to penciclovir.

PDB DOI: https://doi.org/10.2210/pdb7DOI/pdb
NAKB: 7DOI
EM Map EMD-30794: EMDB EMDataResource

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

Deposited: 2020-12-14 Released: 2021-12-15
Deposition Author(s): Li, Z., Yu, X.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Structural basis for repurpose and design of nucleotide drugs for treating COVID-19

Yin, W., Luan, X., Li, Z., Xie, Y., Zhou, Z., Liu, J., Gao, M., Wang, X., Zhou, F., Wang, Q., Wang, Q., Shen, D., Zhang, Y., Tian, G., Aisa, H., Wei, D., Jiang, Y., Xiao, G., Jiang, H., Zhang, L., Yu, X., Shen, J., Zhang, S., Xu, H.

To be published.

Macromolecule Content

Total Structure Weight: 170.81 kDa
Atom Count: 10,128
Modelled Residue Count: 1,222
Deposited Residue Count: 1,452
Unique protein chains: 3
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase	A	943	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b EC: 2.7.7.48
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

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 8	B, F [auth G]	199	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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 7	C	84	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

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 4
Molecule	Chains	Length	Organism	Image
RNA (5'-R(PAPGPAPUPUPAPAPGPUPUPAPU)-3')	D [auth P]	12	Severe acute respiratory syndrome coronavirus 2
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 5
Molecule	Chains	Length	Organism	Image
RNA (5'-R(PCPCPUPAPUPAPAPCPUPUPAPAPUPCP*U)-3')	E [auth T]	15	Severe acute respiratory syndrome coronavirus 2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HCU (Subject of Investigation/LOI) Query on HCU Download Ideal Coordinates CCD File SDF format, chain O [auth P] MOL2 format, chain O [auth P] mmCIF format, chain O [auth P]	O [auth P]	[(2R)-4-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-2-(hydroxymethyl)butyl] dihydrogen phosphate C₁₀ H₁₆ N₅ O₆ P BLURMGIBVBRPQT-ZCFIWIBFSA-N		Interactions Focus chain O [auth P] Interactions & Density Focus chain O [auth P]
POP Query on POP Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain N [auth A] MOL2 format, chain I [auth A] MOL2 format, chain N [auth A] mmCIF format, chain I [auth A] mmCIF format, chain N [auth A]	I [auth A], N [auth A]	PYROPHOSPHATE 2- H₂ O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain N [auth A] Interactions & Density Focus chain I [auth A] Focus chain N [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	G [auth A], H [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
MG (Subject of Investigation/LOI) Query on MG 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] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A]	J [auth A], K [auth A], L [auth A], M [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]