5YQ5 Protein Fibril date Nov 05, 2017
title Crystal Structure Of Human Osteomodulin
authors J.M.M.Caaveiro, T.Tashima, K.Tsumoto
compound source
Molecule: Osteomodulin
Chain: A, B, C, D
Synonym: Keratan Sulfate Proteoglycan Osteomodulin,Kspg Ost Osteoadherin,Osad;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Omd, Slrr2c, Unq190pro216
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
symmetry Space Group: P 1 21 1
R_factor 0.217 R_Free 0.245
length a length b length c angle alpha angle beta angle gamma
75.640 110.700 122.150 90.00 106.97 90.00
method X-Ray Diffractionresolution 2.17 Å
A, D, C, B

Primary referenceMolecular basis for governing the morphology of type-I collagen fibrils by Osteomodulin., Tashima T, Nagatoishi S, Caaveiro JMM, Nakakido M, Sagara H, Kusano-Arai O, Iwanari H, Mimuro H, Hamakubo T, Ohnuma SI, Tsumoto K, Commun Biol. 2018 Apr 19;1:33. doi: 10.1038/s42003-018-0038-2. eCollection 2018. PMID:30271919
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (217 Kb) [Save to disk]
  • Biological Unit Coordinates (5yq5.pdb1.gz) 54 Kb
  • Biological Unit Coordinates (5yq5.pdb2.gz) 54 Kb
  • Biological Unit Coordinates (5yq5.pdb3.gz) 55 Kb
  • Biological Unit Coordinates (5yq5.pdb4.gz) 56 Kb
  • CSU: Contacts of Structural Units for 5YQ5
  • Structure Factors (4949 Kb)
  • Retrieve 5YQ5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5YQ5 from S2C, [Save to disk]
  • View 5YQ5 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 5YQ5
  • 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
  • Fold representative 5yq5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5yq5_B] [5yq5_A] [5yq5_C] [5yq5_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5YQ5
  • Community annotation for 5YQ5 at PDBWiki (http://pdbwiki.org)

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