5W1F Metal Binding Protein date Jun 03, 2017
title Crystal Structure Of Ni(II)- And Ca(II)-Bound Human Calprote
authors T.G.Nakashige, C.L.Drennan, E.M.Nolan
compound source
Molecule: Protein S100-A8
Chain: A, C, G, E
Synonym: Calgranulin-A,Calprotectin L1l Subunit,Cystic Fibr Antigen,Cfag,Leukocyte L1 Complex Light Chain,Migration Inh Factor-Related Protein 8,P8,S100 Calcium-Binding Protein A8 Stone Protein Band A;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: S100a8, Caga, Cfag, Mrp8
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)

Molecule: Protein S100-A9
Chain: B, D, H, F
Synonym: Calgranulin-B,Calprotectin L1h Subunit,Leukocyte L Heavy Chain,Migration Inhibitory Factor-Related Protein 14, Calcium-Binding Protein A9;
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: S100a9, Cagb, Cfag, Mrp14
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
symmetry Space Group: P 21 21 21
R_factor 0.224 R_Free 0.262
crystal
cell
length a length b length c angle alpha angle beta angle gamma
57.020 77.611 222.722 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.60 Å
Gene
Ontology
ChainFunctionProcessComponent
A, E, C, G
  • sequestering of zinc ion

  • F, B, H, D
  • antioxidant activity
  • sequestering of zinc ion

  • Primary referenceNickel Sequestration by the Host-Defense Protein Human Calprotectin., Nakashige TG, Zygiel EM, Drennan CL, Nolan EM, J Am Chem Soc. 2017 Jul 5;139(26):8828-8836. doi: 10.1021/jacs.7b01212. Epub 2017, Jun 22. PMID:28573847
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (280 Kb) [Save to disk]
  • Biological Unit Coordinates (5w1f.pdb1.gz) 138 Kb
  • Biological Unit Coordinates (5w1f.pdb2.gz) 138 Kb
  • CSU: Contacts of Structural Units for 5W1F
  • Structure Factors (813 Kb)
  • Retrieve 5W1F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5W1F from S2C, [Save to disk]
  • Re-refined 5w1f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5W1F 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 5W1F
  • 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
  • Fold representative 5w1f from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5w1f_H] [5w1f_D] [5w1f_F] [5w1f_A] [5w1f_E] [5w1f_G] [5w1f_B] [5w1f_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5W1F
  • Community annotation for 5W1F at PDBWiki (http://pdbwiki.org)

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