1C8M | pdb_00001c8m

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.

Experimental Data Snapshot

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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q82122
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q82122
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q82122
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q82122
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
W11 Query on W11 Download:Ideal Coordinates CCD File SDF format, chain F [auth 1] MOL2 format, chain F [auth 1] mmCIF format, chain F [auth 1]	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		Interactions Focus chain F [auth 1]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth 1] MOL2 format, chain E [auth 1] mmCIF format, chain E [auth 1]	E [auth 1]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth 1]

Experimental Data & Validation

Experimental Data

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

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

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Entry History

Deposition Data

Released Date: 2000-11-22

Deposition Author(s):

Revision History (Full details and data files)

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