3HON Protein Binding date Jun 02, 2009
title Crystal Structure Of Human Collagen Xviii Trimerization Domain (Cubic Form)
authors S.P.Boudko, H.P.Bachinger
compound source
Molecule: Collagen Alpha-1(Xviii) Chain
Chain: A
Fragment: Unp Residues 1441-1496
Synonym: Endostatin
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Col18a1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet23d(+)
symmetry Space Group: I 41 3 2
R_factor 0.279 R_Free 0.288
crystal
cell
length a length b length c angle alpha angle beta angle gamma
94.876 94.876 94.876 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.00 Å
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal Structure of Human Collagen XVIII Trimerization Domain: A Novel Collagen Trimerization Fold., Boudko SP, Sasaki T, Engel J, Lerch TF, Nix J, Chapman MS, Bachinger HP, J Mol Biol. 2009 Jul 23. PMID:19631658
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (14 Kb) [Save to disk]
  • Biological Unit Coordinates (3hon.pdb1.gz) 27 Kb
  • CSU: Contacts of Structural Units for 3HON
  • Structure Factors (13 Kb)
  • Retrieve 3HON in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3HON from S2C, [Save to disk]
  • Re-refined 3hon structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3HON 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 3HON
  • 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 3HON, from MSDmotif at EBI
  • Fold representative 3hon from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3hon_A] [3hon]
  • SWISS-PROT database: [P39060]
  • Domain organization of [COIA1_HUMAN] by SWISSPFAM
  • Alignments of the sequence of 3HON with the sequences similar proteins can be viewed for 3HON's classification [COIA1_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [COIA1_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3HON
  • Community annotation for 3HON 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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