5GTC Structural Protein Dna date Aug 19, 2016
title Crystal Structure Of Complex Between Dmap-Sh Conjugated With Kaposi'S Sarcoma Herpesvirus Lana Peptide (5-15) And Nucleo Particle
authors Y.Arimura, D.Kato, H.Suto, H.Kurumizaka, S.A.Kawashima, K.Yamatsu M.Kanai
compound source
Molecule: Histone H3.1
Chain: A, E
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h3a
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: Histone H4
Chain: B, F
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h4a
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Jm109
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: Histone H2a Type 1-Be
Chain: C, G
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h2ab
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_plasmid: Plasmid

Molecule: Histone H2b Type 1-J
Chain: D, H
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h2bj
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: Dna (146-Mer)
Chain: I, J
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Dh5a
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgem-T-Easy

Molecule: Lana Peptide
Chain: K
Engineered: Yes

Synthetic: Yes
Organism_scientific: Human Herpesvirus 8
Organism_common: Hhv-8
Organism_taxid: 37296
Other_details: Dmap-Sh Conjugated With A Kaposi'S Sarcoma Herpesvirus Lana Peptide (5-15)
symmetry Space Group: P 21 21 21
R_factor 0.211 R_Free 0.267
crystal
cell
length a length b length c angle alpha angle beta angle gamma
107.225 109.017 176.194 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand CL, MN, NH2 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (251 Kb) [Save to disk]
  • Biological Unit Coordinates (5gtc.pdb1.gz) 244 Kb
  • LPC: Ligand-Protein Contacts for 5GTC
  • CSU: Contacts of Structural Units for 5GTC
  • Structure Factors (977 Kb)
  • Retrieve 5GTC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5GTC from S2C, [Save to disk]
  • Re-refined 5gtc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5GTC 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 5GTC
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5gtc from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5gtc_J] [5gtc_K] [5gtc_H] [5gtc_I] [5gtc_C] [5gtc_A] [5gtc_G] [5gtc_D] [5gtc_F] [5gtc_E] [5gtc_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5GTC
  • Community annotation for 5GTC at PDBWiki (http://pdbwiki.org)

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