1SX5 Hydrolase Dna date Mar 30, 2004
title K38a Ecorv Bound To Cleaved Dna And Mn2+: P1 Crystal Form
authors N.C.Horton, J.J.Perona
compound source
Molecule: 5'-D(Apapapgpapt)-3'
Chain: C, E
Engineered: Yes
Synthetic: Yes

Molecule: 5'-D(Paptpcptpt)-3'
Chain: D, F
Engineered: Yes

Synthetic: Yes

Molecule: Type II Restriction Enzyme Ecorv
Chain: A, B
Synonym: Endonuclease Ecorv, R.Ecorv
Engineered: Yes
Mutation: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Ecorvr
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Mm294 (Endi-, Pro-, Thi-, Rk- Mk+);
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pbsrv
symmetry Space Group: P 1
R_factor 0.214 R_Free 0.254
length a length b length c angle alpha angle beta angle gamma
47.708 48.627 63.544 96.68 108.94 107.33
method X-Ray Diffractionresolution 1.50 Å
ligand MN enzyme Hydrolase E.C. BRENDA
note 1SX5 is a representative structure
related structures by homologous chain: 1EON
A, B
  • nuclease activity
  • endonuclease activity

  • Primary referenceDNA Cleavage by EcoRV Endonuclease: Two Metal Ions in Three Metal Ion Binding Sites., Horton NC, Perona JJ, Biochemistry 2004 Jun 8;43(22):6841-57. PMID:15170321
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (100 Kb) [Save to disk]
  • Biological Unit Coordinates (1sx5.pdb1.gz) 94 Kb
  • LPC: Ligand-Protein Contacts for 1SX5
  • CSU: Contacts of Structural Units for 1SX5
  • Likely Quarternary Molecular Structure file(s) for 1SX5
  • Retrieve 1SX5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1SX5 from S2C, [Save to disk]
  • View 1SX5 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 1SX5
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Conformational Epitope Prediction for 1SX5 1SX5A 1SX5B 1SX5C 1SX5D 1SX5E 1SX5F from the CEP Server.
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1SX5, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1sx5a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1sx5b_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1sx5 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: [1sx5_F] [1sx5_B] [1sx5_E] [1sx5_C] [1sx5_D] [1sx5_A] [1sx5]
  • SWISS-PROT database: [P04390]
  • Domain organization of [T2E5_ECOLX] by SWISSPFAM
  • Other resources with information on 1SX5
  • Community annotation for 1SX5 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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