6FXM Transferase date Mar 09, 2018
title Crystal Structure Of Full-Length Human Lysyl Hydroxylase Lh3 Cocrystal With Mn2+
authors L.Scietti, A.Chiapparino, F.De Giorgi, M.Fumagalli, L.Khoriauli, S.Nergadze, S.Basu, V.Olieric, B.Banushi, E.Giulotto, P.Gissen, F
compound source
Molecule: Procollagen-Lysine,2-Oxoglutarate 5-Dioxygenase 3
Chain: A
Synonym: Lysyl Hydroxylase 3,Lh3
Ec: 1.14.11.4
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Plod3
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
Expression_system_cell: Hela
Expression_system_plasmid: Ppuro-Dhfr
symmetry Space Group: C 2 2 21
R_factor 0.229 R_Free 0.252
crystal
cell
length a length b length c angle alpha angle beta angle gamma
97.270 99.949 225.138 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand AKG, FE2, GOL, MN, NAG enzyme Oxidoreductase E.C.1.14.11.4 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceMolecular architecture of the multifunctional collagen lysyl hydroxylase and glycosyltransferase LH3., Scietti L, Chiapparino A, De Giorgi F, Fumagalli M, Khoriauli L, Nergadze S, Basu S, Olieric V, Cucca L, Banushi B, Profumo A, Giulotto E, Gissen P, Forneris F, Nat Commun. 2018 Aug 8;9(1):3163. doi: 10.1038/s41467-018-05631-5. PMID:30089812
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (241 Kb) [Save to disk]
  • Biological Unit Coordinates (6fxm.pdb1.gz) 465 Kb
  • LPC: Ligand-Protein Contacts for 6FXM
  • CSU: Contacts of Structural Units for 6FXM
  • Structure Factors (2673 Kb)
  • Retrieve 6FXM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6FXM from S2C, [Save to disk]
  • View 6FXM 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 6FXM
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6fxm_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6FXM
  • Community annotation for 6FXM at PDBWiki (http://pdbwiki.org)

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