3FD5 Transferase date Nov 25, 2008
title Crystal Structure Of Human Selenophosphate Synthetase 1 Complex With Ampcp
authors K.T.Wang
compound source
Molecule: Selenide, Water Dikinase 1
Chain: A, B
Synonym: Selenophosphate Synthetase 1, Selenium Donor Protein 1;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Sephs1, Seld, Sps, Sps1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 43
R_factor 0.138 R_Free 0.195
length a length b length c angle alpha angle beta angle gamma
66.734 66.734 181.168 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand AP2, K, MG, PO4 enzyme Transferase E.C. BRENDA
A, B

Primary referenceCrystal structures of catalytic intermediates of human selenophosphate synthetase 1., Wang KT, Wang J, Li LF, Su XD, J Mol Biol. 2009 Jul 24;390(4):747-59. Epub 2009 May 25. PMID:19477186
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (231 Kb) [Save to disk]
  • Biological Unit Coordinates (3fd5.pdb1.gz) 223 Kb
  • LPC: Ligand-Protein Contacts for 3FD5
  • CSU: Contacts of Structural Units for 3FD5
  • Structure Factors (645 Kb)
  • Retrieve 3FD5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3FD5 from S2C, [Save to disk]
  • Re-refined 3fd5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3FD5 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 3FD5
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3FD5, from MSDmotif at EBI
  • Fold representative 3fd5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3fd5] [3fd5_A] [3fd5_B]
  • SWISS-PROT database: [P49903]
  • Domain organization of [SPS1_HUMAN] by SWISSPFAM
  • Other resources with information on 3FD5
  • Community annotation for 3FD5 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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