1C8M

REFINED CRYSTAL STRUCTURE OF HUMAN RHINOVIRUS 16 COMPLEXED WITH VP63843 (PLECONARIL), AN ANTI-PICORNAVIRAL DRUG CURRENTLY IN CLINICAL TRIALS

• PDB DOI: https://doi.org/10.2210/pdb1C8M/pdb

• Classification: VIRUS
• Organism(s): rhinovirus A16
• Mutation(s): No 


• Deposited: 2000-05-26 Released: 2000-11-22 
• Deposition Author(s): Chakravarty, S., Bator, C.M., Pevear, D.C., Diana, G.D., Rossmann, M.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.226 
• R-Value Work: 0.219 
• R-Value Observed: 0.243 

Starting Model: experimental

Literature

THE REFINED STRUCTURE OF A PICORNAVIRUS INHIBITOR CURRENTLY IN CLINICAL TRIALS, WHEN COMPLEXED WITH HUMAN RHINOVIRUS 16

CHAKRAVARTY, S., BATOR, C.M., PEVEAR, D.C., DIANA, G.D., ROSSMANN, M.G.

To be published.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Hetero 240-mer - A60B60C60D60 Pseudo Symmetry: Icosahedral - I  (Explore in 3D)
Pseudo Stoichiometry: Hetero 240-mer - A120B60C60 

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

Macromolecule Content

• Total Structure Weight: 95.63 kDa 
• Atom Count: 6,820 
• Modelled Residue Count: 804 
• Deposited Residue Count: 852 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HUMAN RHINOVIRUS 16 COAT PROTEIN	A [auth 1]	285	rhinovirus A16	Mutation(s): 0
UniProt
Find proteins for Q82122 (Human rhinovirus 16) Explore Q82122  Go to UniProtKB:  Q82122

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HUMAN RHINOVIRUS 16 COAT PROTEIN	B [auth 2]	252	rhinovirus A16	Mutation(s): 0
UniProt
Find proteins for Q82122 (Human rhinovirus 16) Explore Q82122  Go to UniProtKB:  Q82122

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HUMAN RHINOVIRUS 16 COAT PROTEIN	C [auth 3]	238	rhinovirus A16	Mutation(s): 0
UniProt
Find proteins for Q82122 (Human rhinovirus 16) Explore Q82122  Go to UniProtKB:  Q82122

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
HUMAN RHINOVIRUS 16 COAT PROTEIN	D [auth 4]	77	rhinovirus A16	Mutation(s): 0
UniProt
Find proteins for Q82122 (Human rhinovirus 16) Explore Q82122  Go to UniProtKB:  Q82122

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
W11	F [auth 1]	3-{3,5-DIMETHYL-4-[3-(3-METHYL-ISOXAZOL-5-YL)-PROPOXY]-PHENYL}-5-TRIFLUOROMETHYL-[1,2,4]OXADIAZOLE C18 H18 F3 N3 O3 KQOXLKOJHVFTRN-UHFFFAOYSA-N
ZN	E [auth 1]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.226 
• R-Value Work: 0.219 
• R-Value Observed: 0.243 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 360.3	α = 90
b = 343.33	β = 90
c = 332.63	γ = 90

Software Package:

Software Name	Purpose
CCP4	model building
X-PLOR	refinement
DENZO	data reduction
SnB	phasing
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-11-22 
Deposition Author(s): Chakravarty, S., Bator, C.M., Pevear, D.C., Diana, G.D., Rossmann, M.G.

Revision History  

• Version 1.0: 2000-11-22
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 2.0: 2023-02-08
  Type: Remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description
• Version 2.1: 2023-03-15
  Changes: Advisory
• Version 2.2: 2023-09-20
  Changes: Data collection, Refinement description