3S5J Transferase date May 23, 2011
title 2.0a Crystal Structure Of Human Phosphoribosyl Pyrophosphate Synthetase 1
authors P.Chen, M.Teng, X.Li
compound source
Molecule: Ribose-Phosphate Pyrophosphokinase 1
Chain: B, A
Synonym: Ppribp, Phosphoribosyl Pyrophosphate Synthase I, P
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Prps1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b
symmetry Space Group: H 3
R_factor 0.215 R_Free 0.256
length a length b length c angle alpha angle beta angle gamma
170.536 170.536 61.778 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.02 Å
ligand SO4 enzyme Transferase E.C. BRENDA
A, B

Primary referenceCrystal and EM Structures of Human Phosphoribosyl Pyrophosphate Synthase I (PRS1) Provide Novel Insights into the Disease-Associated Mutations., Chen P, Liu Z, Wang X, Peng J, Sun Q, Li J, Wang M, Niu L, Zhang Z, Cai G, Teng M, Li X, PLoS One. 2015 Mar 17;10(3):e0120304. doi: 10.1371/journal.pone.0120304., eCollection 2015. PMID:25781187
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (105 Kb) [Save to disk]
  • Biological Unit Coordinates (3s5j.pdb1.gz) 100 Kb
  • LPC: Ligand-Protein Contacts for 3S5J
  • CSU: Contacts of Structural Units for 3S5J
  • Structure Factors (839 Kb)
  • Retrieve 3S5J in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3S5J from S2C, [Save to disk]
  • Re-refined 3s5j structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3S5J 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 3S5J
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3S5J, from MSDmotif at EBI
  • Fold representative 3s5j from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3s5j_A] [3s5j_B] [3s5j]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3S5J: [Pribosyltran_N ] by SMART
  • Other resources with information on 3S5J
  • Community annotation for 3S5J at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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