3RZW Protein Binding date May 12, 2011
title Crystal Structure Of The Monobody Ysmb-9 Bound To Human Sumo
authors R.N.Gilbreth, S.Koide
compound source
Molecule: Monobody Ysmb-9
Chain: A, B
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Sumo1, Smt3c, Smt3h3, Ubl1, Oksw-Cl.43
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Pet24a Derived
Expression_system_plasmid: Phft2

Molecule: Small Ubiquitin-Related Modifier 1
Chain: C, D
Synonym: Sumo-1, Gap-Modifying Protein 1, Gmp1, Smt3 Homolo Sentrin, Ubiquitin-Homology Domain Protein Pic1, Ubiquitin- Protein Smt3c, Smt3c, Ubiquitin-Like Protein Ubl1;
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Pet24a Derived
Expression_system_plasmid: Phft2
symmetry Space Group: C 2 2 21
R_factor 0.186 R_Free 0.237
crystal
cell
length a length b length c angle alpha angle beta angle gamma
93.347 97.829 96.578 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.15 Å
ligand GOL enzyme
Gene
Ontology
ChainFunctionProcessComponent
D, C


Primary referenceTeaching an old scaffold new tricks: monobodies constructed using alternative surfaces of the FN3 scaffold., Koide A, Wojcik J, Gilbreth RN, Hoey RJ, Koide S, J Mol Biol. 2012 Jan 13;415(2):393-405. Epub 2011 Dec 16. PMID:22198408
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (116 Kb) [Save to disk]
  • Biological Unit Coordinates (3rzw.pdb1.gz) 56 Kb
  • Biological Unit Coordinates (3rzw.pdb2.gz) 56 Kb
  • LPC: Ligand-Protein Contacts for 3RZW
  • CSU: Contacts of Structural Units for 3RZW
  • Structure Factors (360 Kb)
  • Retrieve 3RZW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3RZW from S2C, [Save to disk]
  • Re-refined 3rzw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3RZW 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 3RZW
  • 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 3RZW, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3rzw_D] [3rzw] [3rzw_A] [3rzw_B] [3rzw_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3RZW: [FN3] [UBQ ] by SMART
  • Other resources with information on 3RZW
  • Community annotation for 3RZW at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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