3H32 Blood Clotting date Apr 15, 2009
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: Unp Residues 20-216
Synonym: Fibrinopeptide A
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Tissue: Blood Plasma

Molecule: Fibrinogen Beta Chain
Chain: B, E
Fragment: Unp Residues 31-488
Synonym: Fibrinopeptide B

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Tissue: Blood Plasma

Molecule: Fibrinogen Gamma Chain, Isoform Gamma-A
Chain: C, F
Fragment: Unp Residues 27-437

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Tissue: Blood Plasma

Molecule: Fibrin B Knob Pentapeptide
Chain: M, N
Fragment: Unp Residues 22-26
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Peptide Based On The Bovine (Bos T Fibrinopeptide B, P02676, Fibb_bovin, Sequence Position 22-
symmetry Space Group: C 1 2 1
R_factor 0.263 R_Free 0.320
crystal
cell
length a length b length c angle alpha angle beta angle gamma
264.720 97.320 132.490 90.00 122.78 90.00
method X-Ray Diffractionresolution 3.60 Å
ligand CA, GAL, MAN, NAG, SIA enzyme
Gene
Ontology
ChainFunctionProcessComponent
E, B


Primary referenceTwo Families of Synthetic Peptides That Enhance Fibrin Turbidity and Delay Fibrinolysis by Different Mechanisms., Pandi L, Kollman JM, Lopez-Lira F, Burrows JM, Riley M, Doolittle RF, Biochemistry. 2009 Jul 9. PMID:19588915
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (239 Kb) [Save to disk]
  • Biological Unit Coordinates (3h32.pdb1.gz) 228 Kb
  • LPC: Ligand-Protein Contacts for 3H32
  • CSU: Contacts of Structural Units for 3H32
  • Likely Quarternary Molecular Structure file(s) for 3H32
  • Structure Factors (215 Kb)
  • Retrieve 3H32 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3H32 from S2C, [Save to disk]
  • Re-refined 3h32 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3H32 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 3H32
  • 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 3H32, from MSDmotif at EBI
  • Fold representative 3h32 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3h32_D] [3h32_N] [3h32_C] [3h32_A] [3h32_E] [3h32_M] [3h32_B] [3h32] [3h32_F]
  • SWISS-PROT database: [P02671] [P02676] [P02675] [P02679]
  • Domain organization of [FIBA_HUMAN] [FIBB_BOVIN] [FIBB_HUMAN] [FIBG_HUMAN] by SWISSPFAM
  • Domains found in 3H32: [FBG] [Fib_alpha ] by SMART
  • Alignments of the sequence of 3H32 with the sequences similar proteins can be viewed for 3H32's classification [FIBA_HUMAN] [FIBB_BOVIN] [FIBB_HUMAN] [FIBG_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 [FIBA_HUMAN] [FIBB_BOVIN] [FIBB_HUMAN] [FIBG_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3H32
  • Community annotation for 3H32 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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