6M5R Viral Protein date Mar 11, 2020
title The Coordinates Of The Apo Monomeric Terminase Complex
authors Y.X.Yang, P.Yang, N.Wang, Z.H.Chen, Z.H.Zhou, Z.H.Rao, X.X.Wang
compound source
Molecule: Tripartite Terminase Subunit 3
Chain: A
Synonym: Terminase Large Subunit
Ec: 3.1.-.-
Engineered: Yes
Organism_scientific: Human Alphaherpesvirus 1 Strain 17
Organism_common: Hhv-1
Organism_taxid: 10299
Strain: 17
Gene: Trm3, Ul15
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108

Molecule: Tripartite Terminase Subunit 1
Chain: B
Engineered: Yes
Mutation: Yes

Organism_scientific: Human Alphaherpesvirus 1 Strain 17
Organism_common: Hhv-1
Organism_taxid: 10299
Strain: 17
Gene: Trm1, Ul28
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108

Molecule: Tripartite Terminase Subunit 2
Chain: C
Engineered: Yes

Organism_scientific: Human Alphaherpesvirus 1 Strain 17
Organism_common: Hhv-1
Organism_taxid: 10299
Strain: 17
Gene: Ul33, Trm2
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 3.50 Å
ligand ZN enzyme Hydrolase E.C.3.1 BRENDA
Primary referenceArchitecture of the herpesvirus genome-packaging complex and implications for DNA translocation., Yang Y, Yang P, Wang N, Chen Z, Su D, Zhou ZH, Rao Z, Wang X, Protein Cell. 2020 May;11(5):339-351. doi: 10.1007/s13238-020-00710-0. Epub 2020 , Apr 23. PMID:32328903
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (209 Kb) [Save to disk]
  • Biological Unit Coordinates (6m5r.pdb1.gz) 201 Kb
  • LPC: Ligand-Protein Contacts for 6M5R
  • CSU: Contacts of Structural Units for 6M5R
  • Retrieve 6M5R in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6M5R from S2C, [Save to disk]
  • View 6M5R in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 6M5R
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6m5r_A] [6m5r_B] [6m5r_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6M5R
  • Community annotation for 6M5R at PDBWiki (http://pdbwiki.org)

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