7DOI

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


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.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-directed RNA polymerase943Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Non-structural protein 8B,
F [auth G]
199Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Non-structural protein 784Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
RNA (5'-R(P*AP*GP*AP*UP*UP*AP*AP*GP*UP*UP*AP*U)-3')D [auth P]12Severe acute respiratory syndrome coronavirus 2
Sequence Annotations
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  • Reference Sequence

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Entity ID: 5
MoleculeChains LengthOrganismImage
RNA (5'-R(P*CP*CP*UP*AP*UP*AP*AP*CP*UP*UP*AP*AP*UP*CP*U)-3')E [auth T]15Severe acute respiratory syndrome coronavirus 2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HCU (Subject of Investigation/LOI)
Query on HCU

Download Ideal Coordinates CCD File 
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
POP
Query on POP

Download Ideal Coordinates CCD File 
I [auth A],
N [auth A]
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A],
L [auth A],
M [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2021-12-15 
  • Deposition Author(s): Li, Z., Yu, X.

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-15
    Type: Initial release
  • Version 1.1: 2024-06-05
    Changes: Data collection