2Z4E Blood Clotting date Jun 16, 2007
title Crystal Structure Of D-Dimer From Human Fibrin Complexed Wit Arg-Pro-Tyr-Amide
authors R.F.Doolittle, L.Pandi
compound source
Molecule: Fibrinogen Alpha Chain
Chain: A, D
Fragment: Residues In Database 130-218
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Fibrinogen Beta Chain
Chain: B, E
Fragment: Residues In Database 164-491

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Fibrinogen, Gamma Polypeptide
Chain: C, F
Fragment: Residues In Database 114-437

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Fibrin B Knob (Tetrapeptide)
Chain: S, T
Engineered: Yes

Synthetic: Yes
Other_details: The Sequence Occurs Naturally In Humans.

Molecule: Fibrin B Knob (Pentapeptide)
Chain: I, J
Engineered: Yes

Synthetic: Yes
Other_details: The Sequence Occurs Naturally In Bovines (E. Taurus).
symmetry Space Group: P 21 21 21
R_factor 0.216 R_Free 0.275
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.630 148.690 232.680 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand CA, NAG enzyme
Primary referenceProbing the beta-chain hole of fibrinogen with synthetic peptides that differ at their amino termini., Doolittle RF, Pandi L, Biochemistry. 2007 Sep 4;46(35):10033-8. Epub 2007 Aug 10. PMID:17688324
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (207 Kb) [Save to disk]
  • Biological Unit Coordinates (2z4e.pdb1.gz) 199 Kb
  • LPC: Ligand-Protein Contacts for 2Z4E
  • CSU: Contacts of Structural Units for 2Z4E
  • Likely Quarternary Molecular Structure file(s) for 2Z4E
  • Structure Factors (582 Kb)
  • Retrieve 2Z4E in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2Z4E from S2C, [Save to disk]
  • Re-refined 2z4e structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2Z4E 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 2Z4E
  • 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 2Z4E, from MSDmotif at EBI
  • Fold representative 2z4e from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2z4e_I] [2z4e_A] [2z4e_C] [2z4e_T] [2z4e_E] [2z4e_B] [2z4e_J] [2z4e_F] [2z4e_S] [2z4e] [2z4e_D]
  • SWISS-PROT database: [P02671] [P02675] [P02679]
  • Domain organization of [FIBA_HUMAN] [FIBB_HUMAN] [FIBG_HUMAN] by SWISSPFAM
  • Domain found in 2Z4E: [FBG ] by SMART
  • Other resources with information on 2Z4E
  • Community annotation for 2Z4E 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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