3IKM Transferase date Aug 06, 2009
title Crystal Structure Of Human Mitochondrial Dna Polymerase Holo
authors Y.S.Lee, W.D.Kennedy, Y.W.Yin
compound source
Molecule: Dna Polymerase Subunit Gamma-1
Chain: A, D
Fragment: Unp Residues 70-1239
Synonym: Mitochondrial Dna Polymerase Catalytic Subunit, Po
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Dna Polymerase Subunit Gamma-2
Chain: B, C, E, F
Fragment: Unp Residues 59-485
Synonym: Mitochondrial Dna Polymerase Accessory Subunit, Po Mtpolb, Dna Polymerase Gamma Accessory 55 Kda Subunit, P55;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 32
R_factor 0.284 R_Free 0.303
length a length b length c angle alpha angle beta angle gamma
138.394 138.394 226.312 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.24 Å
enzyme Transferase E.C. BRENDA
A, D

F, C, E, B

Primary referenceStructural insight into processive human mitochondrial DNA synthesis and disease-related polymerase mutations., Lee YS, Kennedy WD, Yin YW, Cell. 2009 Oct 16;139(2):312-24. PMID:19837034
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (596 Kb) [Save to disk]
  • Biological Unit Coordinates (3ikm.pdb1.gz) 297 Kb
  • Biological Unit Coordinates (3ikm.pdb2.gz) 297 Kb
  • CSU: Contacts of Structural Units for 3IKM
  • Structure Factors (474 Kb)
  • Retrieve 3IKM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3IKM from S2C, [Save to disk]
  • Re-refined 3ikm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3IKM 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 3IKM
  • 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
  • 3D motif for 3IKM, from MSDmotif at EBI
  • Fold representative 3ikm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ikm_E] [3ikm_A] [3ikm] [3ikm_F] [3ikm_B] [3ikm_C] [3ikm_D]
  • SWISS-PROT database: [P54098] [Q9UHN1]
  • Domain organization of [DPOG1_HUMAN] [DPOG2_HUMAN] by SWISSPFAM
  • Domain found in 3IKM: [POLAc ] by SMART
  • Other resources with information on 3IKM
  • Community annotation for 3IKM at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science