1D3K Metal Transport date Sep 29, 1999
title Human Serum Transferrin
authors H.W.Yang, R.T.A.Macgillivray, J.Chen, Y.Luo, Y.Wang, G.D.Brayer, A.Mason, R.C.Woodworth, M.E.P.Murphy
compound source
Molecule: Serum Transferrin
Chain: A
Fragment: N-Terminal Lobe
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Tissue: Blood
Expression_system: Cricetinae
Expression_system_common: Hamsters
Expression_system_taxid: 10026
Expression_system_organ: Kidney
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pnut-Bhk
symmetry Space Group: P 21 21 21
R_factor 0.184 R_Free 0.225
length a length b length c angle alpha angle beta angle gamma
45.010 57.810 135.600 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand CO3, FE enzyme
related structures by homologous chain: 1A8E, 1FQE

Primary referenceCrystal structures of two mutants (K206Q, H207E) of the N-lobe of human transferrin with increased affinity for iron., Yang AH, MacGillivray RT, Chen J, Luo Y, Wang Y, Brayer GD, Mason AB, Woodworth RC, Murphy ME, Protein Sci 2000 Jan;9(1):49-52. PMID:10739246
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (59 Kb) [Save to disk]
  • Biological Unit Coordinates (1d3k.pdb1.gz) 55 Kb
  • LPC: Ligand-Protein Contacts for 1D3K
  • CSU: Contacts of Structural Units for 1D3K
  • Likely Quarternary Molecular Structure file(s) for 1D3K
  • Structure Factors (292 Kb)
  • Retrieve 1D3K in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1D3K from S2C, [Save to disk]
  • Re-refined 1d3k structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1D3K 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 1D3K
  • 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 1D3K, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1d3ka_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1d3k from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1d3k_A] [1d3k]
  • SWISS-PROT database: [P02787]
  • Domain organization of [TRFE_HUMAN] by SWISSPFAM
  • Domain found in 1D3K: [TR_FER ] by SMART
  • Other resources with information on 1D3K
  • Community annotation for 1D3K 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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