3H4D Replication Dna date Apr 18, 2009
title Ternary Complex Of Human Dna Polymerase Iota With Template U Incoming Dgtp
authors R.Jain, D.T.Nair, R.E.Johnson, L.Prakash, S.Prakash, A.K.Aggarwal
compound source
Molecule: Dna Polymerase Iota
Chain: A
Fragment: Polymerase Iota
Synonym: Rad30 Homolog B, Eta2
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Poli, Rad30b
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

Molecule: 5'-D(Apgpgpapcpcp(Doc))
Chain: P
Fragment: Primer Dna Strand
Engineered: Yes
Other_details: Primer Dna Strand

Synthetic: Yes

Molecule: 5'-D(Tp(Bru)Pgpgpgptpcpcpt)
Chain: T
Fragment: Template Dna Strand
Engineered: Yes
Other_details: Template Dna Strand

Synthetic: Yes
symmetry Space Group: P 65 2 2
R_factor 0.254 R_Free 0.270
length a length b length c angle alpha angle beta angle gamma
97.915 97.915 203.392 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.20 Å
ligand BRU, DGT, DOC, MG enzyme Transferase E.C. BRENDA

Primary referenceReplication across template T/U by human DNA polymerase-iota., Jain R, Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK, Structure. 2009 Jul 15;17(7):974-80. PMID:19604477
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (78 Kb) [Save to disk]
  • Biological Unit Coordinates (3h4d.pdb1.gz) 71 Kb
  • LPC: Ligand-Protein Contacts for 3H4D
  • CSU: Contacts of Structural Units for 3H4D
  • Likely Quarternary Molecular Structure file(s) for 3H4D
  • Structure Factors (185 Kb)
  • Retrieve 3H4D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3H4D from S2C, [Save to disk]
  • Re-refined 3h4d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3H4D 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 3H4D
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3H4D, from MSDmotif at EBI
  • Fold representative 3h4d from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3h4d_P] [3h4d_A] [3h4d_T] [3h4d]
  • SWISS-PROT database: [Q9UNA4]
  • Domain organization of [POLI_HUMAN] by SWISSPFAM
  • Other resources with information on 3H4D
  • Community annotation for 3H4D at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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