2G4D Hydrolase Protein Binding date Feb 22, 2006
title Crystal Structure Of Human Senp1 Mutant (C603s) In Complex W
authors Z.Xu, S.F.Chau, K.H.Lam, S.W.N.Au
compound source
Molecule: Senp1 Protein
Chain: A, C
Fragment: Protease Catalytic Domain
Synonym: Sentrin-Specific Protease 1
Ec: 3.4.22.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ptwoe

Molecule: Small Ubiquitin-Related Modifier 1
Chain: B, D
Fragment: Residues 20-97
Synonym: Sumo-1, Ubiquitin-Like Protein Smt3c, Smt3 Homolog Ubiquitin-Homology Domain Protein Pic1, Ubiquitin-Like Prot Gap-Modifying Protein 1, Gmp1, Sentrin;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28
symmetry Space Group: P 43
R_factor 0.248 R_Free 0.278
crystal
cell
length a length b length c angle alpha angle beta angle gamma
97.308 97.308 102.580 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand
enzyme Hydrolase E.C.3.4.22 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C


Primary referenceCrystal structure of the SENP1 mutant C603S-SUMO complex reveals the hydrolytic mechanism of SUMO-specific protease., Xu Z, Chau SF, Lam KH, Chan HY, Ng TB, Au SW, Biochem J. 2006 Sep 15;398(3):345-52. PMID:16712526
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (92 Kb) [Save to disk]
  • Biological Unit Coordinates (2g4d.pdb1.gz) 45 Kb
  • Biological Unit Coordinates (2g4d.pdb2.gz) 44 Kb
  • CSU: Contacts of Structural Units for 2G4D
  • Likely Quarternary Molecular Structure file(s) for 2G4D
  • Structure Factors (192 Kb)
  • Retrieve 2G4D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2G4D from S2C, [Save to disk]
  • Re-refined 2g4d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2G4D 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 2G4D
  • 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 2G4D, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2g4d_A] [2g4d_C] [2g4d_D] [2g4d_B] [2g4d]
  • SWISS-PROT database: [Q9P0U3] [P63165]
  • Domain organization of [SENP1_HUMAN] [SUMO1_HUMAN] by SWISSPFAM
  • Domain found in 2G4D: [UBQ ] by SMART
  • Other resources with information on 2G4D
  • Community annotation for 2G4D 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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