1ODB Metal Binding Protein date Feb 15, 2003
title The Crystal Structure Of Human S100a12 - Copper Complex
authors O.V.Moroz, A.A.Antson, S.J.Grist, N.J.Maitland, G.G.Dodson, K.S.W E.M.Lukanidin, I.B.Bronstein
compound source
Molecule: Calgranulin C
Chain: A, B, C, D, E, F
Synonym: S100a12, Cagc, P6, Cgrp, Neutrophil S100 Protein, Binding Protein In Amniotic Fluid 1, Caaf1;
Engineered: Yes
Other_details: Ca2+ And Cu2+ Bound Form
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Tissue: Blood
Cell: Granulocyte
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 2
R_factor 0.186 R_Free 0.226
crystal
cell
length a length b length c angle alpha angle beta angle gamma
70.569 118.957 90.185 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.19 Å
ligand CA, CU enzyme
related structures by homologous chain: 1E8A, 1GQM
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B


Primary referenceStructure of the human S100A12-copper complex: implications for host-parasite defence., Moroz OV, Antson AA, Grist SJ, Maitland NJ, Dodson GG, Wilson KS, Lukanidin E, Bronstein IB, Acta Crystallogr D Biol Crystallogr 2003 May;59(Pt 5):859-67. PMID:12777802
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (99 Kb) [Save to disk]
  • Biological Unit Coordinates (1odb.pdb1.gz) 32 Kb
  • Biological Unit Coordinates (1odb.pdb2.gz) 31 Kb
  • Biological Unit Coordinates (1odb.pdb3.gz) 33 Kb
  • LPC: Ligand-Protein Contacts for 1ODB
  • CSU: Contacts of Structural Units for 1ODB
  • Likely Quarternary Molecular Structure file(s) for 1ODB
  • Structure Factors (561 Kb)
  • Retrieve 1ODB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1ODB from S2C, [Save to disk]
  • Re-refined 1odb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1ODB 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 1ODB
  • 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 1ODB, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1odba_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1odbb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1odbc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1odbd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1odbe_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1odbf_, region F [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: [1odb] [1odb_F] [1odb_C] [1odb_A] [1odb_E] [1odb_B] [1odb_D]
  • SWISS-PROT database: [P80511]
  • Domain organization of [S10AC_HUMAN] by SWISSPFAM
  • Domain found in 1ODB: [S_100 ] by SMART
  • Other resources with information on 1ODB
  • Community annotation for 1ODB 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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