5ZIU | pdb_00005ziu

Crystal structure of human Entervirus D68 RdRp

• PDB DOI: https://doi.org/10.2210/pdb5ZIU/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): enterovirus D68
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-03-17 Released: 2019-04-17 
• Deposition Author(s): Wang, M.L., Zhang, Y., Chen, Y.P., Lu, D.R., Jiang, H., Chen, Y.J., Li, L., Zhang, C.H., Shi, Q.L., Su, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.266 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human Entervirus D68 RdRp in complex with NADPH

Wang, M.L., Zhang, Y., Dou, Y.S., Chen, Y.P., Lu, D.R., Jiang, H., Chen, Y.J., Li, L., Zhang, C.H., Shi, Q.L., Su, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 52.51 kDa 
• Atom Count: 3,853 
• Modeled Residue Count: 457 
• Deposited Residue Count: 457 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RdRp	A	457	enterovirus D68	Mutation(s): 0
UniProt
Find proteins for I6TFG7 (Human enterovirus D68) Explore I6TFG7  Go to UniProtKB:  I6TFG7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	E [auth A], F [auth A], G [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	B [auth A], C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.266 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.835	α = 90
b = 59.835	β = 90
c = 358.923	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-04-17 
Deposition Author(s): Wang, M.L., Zhang, Y., Chen, Y.P., Lu, D.R., Jiang, H., Chen, Y.J., Li, L., Zhang, C.H., Shi, Q.L., Su, D.

Revision History  

• Version 1.0: 2019-04-17
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description