1RYO Metal Transport date Dec 22, 2003
title Human Serum Transferrin, N-Lobe Bound With Oxalate
authors P.J.Halbrooks, A.B.Mason, T.E.Adams, S.K.Briggs, S.J.Everse
compound source
Molecule: Serotransferrin
Chain: A
Fragment: N-Terminal Lobe (Residues 20-346)
Synonym: Transferrin, Siderophilin, Beta-1-Metal Binding Gl Pro1400;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tf
Expression_system: Mesocricetus Auratus
Expression_system_common: Golden Hamster
Expression_system_taxid: 10036
Expression_system_organ: Kidney
Expression_system_vector_type: Pnut
symmetry Space Group: P 21 21 21
R_factor 0.221 R_Free 0.235
crystal
cell
length a length b length c angle alpha angle beta angle gamma
44.092 57.252 135.988 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.20 Å
ligand FE, OXL enzyme
related structures by homologous chain: 1A8E
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceThe oxalate effect on release of iron from human serum transferrin explained., Halbrooks PJ, Mason AB, Adams TE, Briggs SK, Everse SJ, J Mol Biol 2004 May 21;339(1):217-26. PMID:15123433
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (65 Kb) [Save to disk]
  • Biological Unit Coordinates (1ryo.pdb1.gz) 60 Kb
  • LPC: Ligand-Protein Contacts for 1RYO
  • CSU: Contacts of Structural Units for 1RYO
  • Likely Quarternary Molecular Structure file(s) for 1RYO
  • Structure Factors (846 Kb)
  • Retrieve 1RYO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1RYO from S2C, [Save to disk]
  • Re-refined 1ryo structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1RYO 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 1RYO
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Conformational Epitope Prediction for 1RYO from the CEP Server.
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1RYO, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ryoa_, region A [Jmol] [rasmolscript] [script source]
  • 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: [1ryo_A] [1ryo]
  • SWISS-PROT database: [P02787]
  • Domain organization of [TRFE_HUMAN] by SWISSPFAM
  • Domain found in 1RYO: [TR_FER ] by SMART
  • Other resources with information on 1RYO
  • Community annotation for 1RYO 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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