PDBsum entry 2rs3

Virus

PDB id

2rs3

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Contents

			Protein chains

					273 a.a. *


					255 a.a. *


					236 a.a. *


					40 a.a. *

			Ligands

					W59

			Waters ×4

* Residue conservation analysis

PDB id:

2rs3

Links

Name:

Virus

Title:

Structural analysis of antiviral agents that interact with the capsid of human rhinoviruses

Structure:

Human rhinovirus 14 coat protein (subunit vp1). Chain: 1. Engineered: yes. Human rhinovirus 14 coat protein (subunit vp2). Chain: 2. Engineered: yes. Human rhinovirus 14 coat protein (subunit vp3). Chain: 3. Engineered: yes.

Source:

Human rhinovirus 14. Organism_taxid: 12131. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: hela cells. Expression_system_cell_line: hela cells

Resolution:

3.00Å

R-factor:

not given

Authors:

J.Badger,T.J.Smith,M.G.Rossmann

Key ref:

J.Badger et al. (1989). Structural analysis of antiviral agents that interact with the capsid of human rhinoviruses. Proteins, 6, 1. PubMed id: 2558377

Date:

03-Oct-88

Release date:

15-Jan-90

Supersedes:

1rs3

PROCHECK

	Headers

	References

Protein chain

P03303 (POLG_HRV14) - Genome polyprotein from Human rhinovirus 14

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:					2179 a.a. 273 a.a.

Protein chain

P03303 (POLG_HRV14) - Genome polyprotein from Human rhinovirus 14

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:					2179 a.a. 255 a.a.*

Protein chain

P03303 (POLG_HRV14) - Genome polyprotein from Human rhinovirus 14

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:					2179 a.a. 236 a.a.

Protein chain

P03303 (POLG_HRV14) - Genome polyprotein from Human rhinovirus 14

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:					2179 a.a. 40 a.a.

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 1 residue position (black cross)



		Enzyme reactions

Enzyme class 2:

Chains 1, 2, 3, 4: E.C.2.7.7.48 - RNA-directed Rna polymerase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate

RNA(n)	+	ribonucleoside 5'-triphosphate	=	RNA(n+1)	+	diphosphate

Enzyme class 3:

Chains 1, 2, 3, 4: E.C.3.4.22.28 - picornain 3C.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.

Enzyme class 4:

Chains 1, 2, 3, 4: E.C.3.4.22.29 - picornain 2A.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

Selective cleavage of Tyr-|-Gly bond in the picornavirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.

Enzyme class 5:

Chains 1, 2, 3, 4: E.C.3.6.1.15 - nucleoside-triphosphate phosphatase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + phosphate + H⁺

ribonucleoside 5'-triphosphate	+	H2O	=	ribonucleoside 5'-diphosphate	+	phosphate	+	H(+)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

	Proteins 6:1 (1989)
PubMed id: 2558377

Structural analysis of antiviral agents that interact with the capsid of human rhinoviruses.
J.Badger, I.Minor, M.A.Oliveira, T.J.Smith, M.G.Rossmann.

ABSTRACT

X-Ray diffraction data have been obtained for nine related antiviral agents ("WIN compounds") while bound to human rhinovirus 14 (HRV14). These compounds can inhibit both viral attachment to host cells and uncoating. To calculate interpretable electron density maps it was necessary to account for (1) the low (approximately 60%) occupancies of these compounds in the crystal, (2) the large (up to 7.9 A) conformational changes induced at the attachment site, and (3) the incomplete diffraction data. Application of a density difference map technique, which exploits the 20-fold noncrystallographic redundancy in HRV14, resulted in clear images of the HRV14:WIN complexes. A real-space refinement procedure was used to fit atomic models to these maps. The binding site of WIN compounds in HRV14 is a hydrophobic pocket composed mainly from residues that form the beta-barrel of VP1. Among rhinoviruses, the residues associated with the binding pocket are far more conserved than external residues and are mostly contained within regular secondary structural elements. Molecular dynamics simulations of three HRV14:WIN complexes suggest that portions of the WIN compounds and viral protein near the entrance of the binding pocket are more flexible than portions deeper within the beta-barrel.

Literature references that cite this PDB file's key reference

PubMed id

Reference

19714577

J.M.Rollinger, and M.Schmidtke (2011).
The human rhinovirus: human-pathological impact, mechanisms of antirhinoviral agents, and strategies for their discovery.

Med Res Rev, 31, 42-92.

20831240

S.L.Chan, and P.Labute (2010).
Training a scoring function for the alignment of small molecules.

J Chem Inf Model, 50, 1724-1735.

17334823

K.H.Kim (2007).
Outliers in SAR and QSAR: is unusual binding mode a possible source of outliers?

J Comput Aided Mol Des, 21, 63-86.

15883190

L.Wang, and D.L.Smith (2005).
Capsid structure and dynamics of a human rhinovirus probed by hydrogen exchange mass spectrometry.

Protein Sci, 14, 1661-1672.

10651041

B.B.Goldman, and W.T.Wipke (2000).
QSD quadratic shape descriptors. 2. Molecular docking using quadratic shape descriptors (QSDock).

Proteins, 38, 79-94.

10611281

A.T.Hadfield, G.D.Diana, and M.G.Rossmann (1999).
Analysis of three structurally related antiviral compounds in complex with human rhinovirus 16.

Proc Natl Acad Sci U S A, 96, 14730-14735.

PDB codes:

1qju 1qjx 1qjy

10562537

P.R.Kolatkar, J.Bella, N.H.Olson, C.M.Bator, T.S.Baker, and M.G.Rossmann (1999).
Structural studies of two rhinovirus serotypes complexed with fragments of their cellular receptor.

EMBO J, 18, 6249-6259.

PDB codes:

1d3e 1d3i 1d3l

9294865

D.Joseph-McCarthy, J.M.Hogle, and M.Karplus (1997).
Use of the multiple copy simultaneous search (MCSS) method to design a new class of picornavirus capsid binding drugs.

Proteins, 29, 32-58.

9253417

M.W.Wien, S.Curry, D.J.Filman, and J.M.Hogle (1997).
Structural studies of poliovirus mutants that overcome receptor defects.

Nat Struct Biol, 4, 666-674.

PDB codes:

1al2 1ar6 1ar7 1ar8 1ar9 1asj

8591043

J.K.Muckelbauer, M.Kremer, I.Minor, G.Diana, F.J.Dutko, J.Groarke, D.C.Pevear, and M.G.Rossmann (1995).
The structure of coxsackievirus B3 at 3.5 A resolution.

Structure, 3, 653-667.

7820548

R.A.Grant, C.N.Hiremath, D.J.Filman, R.Syed, K.Andries, and J.M.Hogle (1994).
Structures of poliovirus complexes with anti-viral drugs: implications for viral stability and drug design.

Curr Biol, 4, 784-797.

PDB codes:

1vba 1vbb 1vbc 1vbd 1vbe

7915182

M.A.Oliveira, R.Zhao, W.M.Lee, M.J.Kremer, I.Minor, R.R.Rueckert, G.D.Diana, D.C.Pevear, F.J.Dutko, and M.A.McKinlay (1993).
The structure of human rhinovirus 16.

Structure, 1, 51-68.

PDB codes:

1ayn 2rhn

1528078

M.D.Walkinshaw (1992).
Protein targets for structure-based drug design.

Med Res Rev, 12, 317-372.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.