3G53 Oxygen Binding date Feb 04, 2009
title Ligand Migration And Cavities Within Scapharca Dimeric Hemog Wild Type With Co Bound To Heme And Chloropropyl Benzene Bo Xe4 Cavity
authors J.E.Knapp, R.Pahl, J.Cohen, J.C.Nichols, K.Schulten, Q.H.Gibson, V W.E.Royer Jr.
compound source
Molecule: Globin-1
Chain: A, B
Synonym: Dimeric Hemoglobin,Globin I,Hbi
Engineered: Yes
 Organism_scientific: Anadara Inaequivalvis
Organism_common: Inequivalve Ark
Organism_taxid: 6561
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: W3110laciql8
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcs-26
symmetry Space Group: C 1 2 1
R_factor 0.189 R_Free 0.204
crystal
cell
length a length b length c angle alpha angle beta angle gamma
93.190 43.870 83.350 90.00 121.88 90.00
method X-Ray Diffractionresolution 1.64 Å
ligand CMO, HEM, LT1 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceLigand migration and cavities within Scapharca Dimeric HbI: studies by time-resolved crystallo-graphy, Xe binding, and computational analysis., Knapp JE, Pahl R, Cohen J, Nichols JC, Schulten K, Gibson QH, Srajer V, Royer WE Jr, Structure. 2009 Nov 11;17(11):1494-504. PMID:19913484
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (55 Kb) [Save to disk]
  • Biological Unit Coordinates (3g53.pdb1.gz) 50 Kb
  • LPC: Ligand-Protein Contacts for 3G53
  • CSU: Contacts of Structural Units for 3G53
  • Structure Factors (282 Kb)
  • Retrieve 3G53 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3G53 from S2C, [Save to disk]
  • Re-refined 3g53 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3G53 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 3G53
  • 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
  • 3D motif for 3G53, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3g53_A] [3g53_B] [3g53]
  • SWISS-PROT database: [P02213]
  • Domain organization of [GLB1_SCAIN] by SWISSPFAM
    • Other resources with information on 3G53
  • Community annotation for 3G53 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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