5FNA Hydrolase date Nov 11, 2015
title Cryo-Em Reconstruction Of Caspase-1 Card
authors Y.Li, A.Lu, F.I.Schmidt, Q.Yin, S.Chen, T.M.Fu, A.B.Tong, H.L.Ploeg H.Wu
compound source
Molecule: Caspase-1
Chain: A, B, C, D, E, F, G, H
Fragment: Card Domain
Synonym: Casp-1,Interleukin-1 Beta Convertase,Il-1bc,Interl Beta-Converting Enzyme,Il-1 Beta-Converting Enzyme,P45;
Ec: 3.4.22.36
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Casp1, Il1bc, Il1bce
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_plasmid: Pdb-His-Mbp
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 4.80 Å
ligand
enzyme Hydrolase E.C.3.4.22.36 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, A, E, B, H, C, D, G


Primary referenceMolecular basis of caspase-1 polymerization and its inhibition by a new capping mechanism., Lu A, Li Y, Schmidt FI, Yin Q, Chen S, Fu TM, Tong AB, Ploegh HL, Mao Y, Wu H, Nat Struct Mol Biol. 2016 May;23(5):416-25. doi: 10.1038/nsmb.3199. Epub 2016 Apr, 4. PMID:27043298
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (105 Kb) [Save to disk]
  • Biological Unit Coordinates (5fna.pdb1.gz) 103 Kb
  • CSU: Contacts of Structural Units for 5FNA
  • Retrieve 5FNA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5FNA from S2C, [Save to disk]
  • View 5FNA 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 5FNA
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5fna_G] [5fna_E] [5fna_A] [5fna_C] [5fna_B] [5fna] [5fna_D] [5fna_F] [5fna_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5FNA: [CARD ] by SMART
  • Other resources with information on 5FNA
  • Community annotation for 5FNA at PDBWiki (http://pdbwiki.org)

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