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1C8M
Biol. Unit 1
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Asym.Unit (147 KB)
Biol.Unit 1, α-C (8.0 MB)
Biol.Unit 1 (8.0 MB)
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(1)
Title
:
REFINED CRYSTAL STRUCTURE OF HUMAN RHINOVIRUS 16 COMPLEXED WITH VP63843 (PLECONARIL), AN ANTI-PICORNAVIRAL DRUG CURRENTLY IN CLINICAL TRIALS
Authors
:
S. Chakravarty, C. M. Bator, D. C. Pevear, G. D. Diana, M. G. Rossmann
Date
:
26 May 00 (Deposition) - 22 Nov 00 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : 1,2,3,4
Biol. Unit 1: 1,2,3,4 (60x)
Keywords
:
Rhinovirus Coat Protein, Human Rhinovirus 16, Antiviral Compound, Drug, Win Compound, Icosahedral Virus
(Keyword Search:
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Reference
:
S. Chakravarty, C. M. Bator, D. C. Pevear, G. D. Diana, M. G. Rossmann
The Refined Structure Of A Picornavirus Inhibitor Currently In Clinical Trials, When Complexed With Human Rhinovirus 16
To Be Published
(for further references see the
PDB file header
)
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Hetero Components
(1, 60)
Info
All Hetero Components
1a: 3-{3,5-DIMETHYL-4-[3-(3-METHYL-ISO... (W11a)
2a: ZINC ION (ZNa)
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No.
Name
Count
Type
Full Name
1
W11
60
Ligand/Ion
3-{3,5-DIMETHYL-4-[3-(3-METHYL-ISOXAZOL-5-YL)-PROPOXY]-PHENYL}-5-TRIFLUOROMETHYL-[1,2,4]OXADIAZOLE
2
ZN
-1
Ligand/Ion
ZINC ION
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Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: ION (AUTHOR)
4: POC (AUTHOR)
5: RNA (AUTHOR)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS 1:134
BINDING SITE FOR RESIDUE ZN 1 6000
2
AC2
SOFTWARE
ILE 1:77 , ILE 1:98 , LEU 1:100 , MET 1:124 , TYR 1:142 , MET 1:143 , TYR 1:144 , ALA 1:166 , VAL 1:168 , PHE 1:179 , LEU 1:181 , LEU 1:184 , TYR 1:190 , ASN 1:212 , MET 1:214 , LEU 1:217 , HOH 1:5378
BINDING SITE FOR RESIDUE W11 1 7001
3
ION
AUTHOR
HIS 1:134 , HIS 1:228 , ZN 1:6000
PUTATIVE ZINC BINDING SITE ON ICOSAHEDRAL FIVE-FOLD AXIS. ION LIGANDED BY FIVE SYMMETRY RELATED HISTIDINES (HIS 1 134). EXTERIOR OF SITE SURROUNDED BY A WIDER CIRCLE OF FIVE HISTIDINES (HIS 2 228)
4
POC
AUTHOR
PHE 1:179 , MET 1:214 , LEU 1:217 , W11 1:7001
AN ANTIVIRAL COMPOUND IS FOUND IN A POCKET OF VP1
5
RNA
AUTHOR
TRP 2:38 , PHE 3:35
RNA OBSERVED INTERACTING WITH THESE RESIDUES ON THE INTERIOR SURFACE OF VIRAL PROTEIN CAPSID. NON- CONSERVATIVE MUTATION OF TRP 2 38 GIVES NON-VIABLE VIRUS.
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SAPs(SNPs)/Variants
(0, 0)
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Exons
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SCOP Domains
(1, 3)
Info
All SCOP Domains
1a: SCOP_d1c8m_1 (4:,2:)
1b: SCOP_d1c8m1_ (1:)
1c: SCOP_d1c8m3_ (3:)
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(
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Organisms
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)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Nucleoplasmin-like/VP (viral coat and capsid proteins)
(278)
Superfamily
:
Positive stranded ssRNA viruses
(163)
Family
:
Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
(103)
Protein domain
:
Rhinovirus coat proteins
(46)
Human rhinovirus 16, (HRV-16) [TaxId: 31708]
(9)
1a
d1c8m.1
4:,2:
1b
d1c8m1_
1:
1c
d1c8m3_
3:
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1c8m400 (4:1-44)
2a: CATH_1c8m300 (3:1-238)
2b: CATH_1c8m200 (2:10-261)
2c: CATH_1c8m100 (1:1-285)
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Organisms
(
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(
)
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Rhinovirus 14, subunit 4
(101)
Homologous Superfamily
:
Rhinovirus 14, subunit 4
(68)
Human rhinovirus 16. Organism_taxid: 31708. Strain: serotype 16. Humanrhinovirus 16. Organism_taxid: 31708. Strain: serotype 16. Human rhinovirus 16. Organism_taxid: 31708. Strain: serotype 16.
(1)
1a
1c8m400
4:1-44
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
[code=2.60.120.20, no name defined]
(133)
Human rhinovirus 16. Organism_taxid: 31708. Strain: serotype 16. Humanrhinovirus 16. Organism_taxid: 31708. Strain: serotype 16. Human rhinovirus 16. Organism_taxid: 31708. Strain: serotype 16.
(1)
2a
1c8m300
3:1-238
2b
1c8m200
2:10-261
2c
1c8m100
1:1-285
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Pfam Domains
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Asym.Unit (147 KB)
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