PDBsum entry: 3dpr

Virus

PDB id: 3dpr

Contents

Protein chains

269 a.a. *

250 a.a. *

237 a.a. *

25 a.a. *

39 a.a. *

Ligands

DAO

Metals

_CA

* Residue conservation analysis

PDB id:

3dpr

Name:

Virus

Title:

Human rhinovirus 2 bound to a concatamer of the vldl receptor module v3

Structure:

Protein vp1. Chain: a. Synonym: virion protein 1, p1d, coat protein vp1. Protein vp2. Chain: b. Synonym: virion protein 2, p1b, coat protein vp2. Protein vp3. Chain: c. Synonym: virion protein 3, p1c, coat protein vp3.

Source:

Human rhinovirus 2. Hrv-2. Organism_taxid: 12130. Strain: human. Other_details: hela cells. Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli.

Resolution:

3.50Å R-factor: 0.426 R-free: 0.441

Authors:

J.Querol-Audi,J.Pous,I.Fita,N.Verdaguer

Date:

09-Jul-08 Release date: 07-Apr-09

Protein chain

P04936  (POLG_HRV2) -  Genome polyprotein

Seq: 2150 a.a.

Struc: 269 a.a.

Protein chain

P04936  (POLG_HRV2) -  Genome polyprotein

Seq: 2150 a.a.

Struc: 250 a.a.

Protein chain

P04936  (POLG_HRV2) -  Genome polyprotein

Seq: 2150 a.a.

Struc: 237 a.a.

Protein chain

P04936  (POLG_HRV2) -  Genome polyprotein

Seq: 2150 a.a.

Struc: 25 a.a.*

Protein chain

P98155  (VLDLR_HUMAN) -  Very low-density lipoprotein receptor

Seq: 873 a.a.

Struc: 39 a.a.

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: Chains A, B, C, D: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
• Enzyme class 2: Chains A, B, C, D: E.C.3.4.22.28 - Picornain 3C.
• 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 3: Chains A, B, C, D: E.C.3.4.22.29 - Picornain 2A.
• 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 4: Chains A, B, C, D: E.C.3.6.1.15 - Nucleoside-triphosphatase.
• Reaction: NTP + H₂O = NDP + phosphate

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

 Gene Ontology (GO) functional annotation 

• Cellular component: viral capsid (1 term)
• Biochemical function: structural molecule activity (1 term)