2A45 Hydrolase Hydrolase Inhibitor date Jun 27, 2005
title Crystal Structure Of The Complex Between Thrombin And The Ce Region Of Fibrin
authors I.Pechik, J.Madrazo, G.L.Gilliland, L.Medved
compound source
Molecule: Thrombin Light Chain
Chain: A, D
Synonym: Coagulation Factor II
Ec: 3.4.21.5
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Thrombin Heavy Chain
Chain: B, E
Synonym: Coagulation Factor II
Ec: 3.4.21.5

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Fibrinogen Alpha Chain
Chain: G, J
Fragment: Unp P02671, Residues 36-92

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: Proteolytic Fragment

Molecule: Fibrinogen Beta Chain
Chain: H, K

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: Proteolytic Fragment

Molecule: Fibrinogen Gamma Chain
Chain: I, L

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: Proteolytic Fragment
symmetry Space Group: P 31
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
76.263 76.263 192.452 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.65 Å
ligand 0G6, ARM, DPN, PO4 enzyme Hydrolase E.C.3.4.21.5 BRENDA
note 2A45 (Molecule of the Month:pdb83)supersedes 1QVH
Gene
Ontology
ChainFunctionProcessComponent
A, D


E, B


J, K, H, I, G, L


Primary referenceStructural basis for sequential cleavage of fibrinopeptides upon fibrin assembly., Pechik I, Yakovlev S, Mosesson MW, Gilliland GL, Medved L, Biochemistry. 2006 Mar 21;45(11):3588-97. PMID:16533041
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (128 Kb) [Save to disk]
  • Biological Unit Coordinates (2a45.pdb1.gz) 120 Kb
  • LPC: Ligand-Protein Contacts for 2A45
  • CSU: Contacts of Structural Units for 2A45
  • Likely Quarternary Molecular Structure file(s) for 2A45
  • Structure Factors (297 Kb)
  • Retrieve 2A45 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2A45 from S2C, [Save to disk]
  • Re-refined 2a45 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2A45 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 2A45
  • 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
  • 3D motif for 2A45, from MSDmotif at EBI
  • Fold representative 2a45 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2a45_G] [2a45_J] [2a45_B] [2a45_I] [2a45_L] [2a45] [2a45_K] [2a45_H] [2a45_A] [2a45_D] [2a45_F] [2a45_C] [2a45_E]
  • SWISS-PROT database: [P02671] [P02675] [P02679] [P00734]
  • Domain organization of [FIBA_HUMAN] [FIBB_HUMAN] [FIBG_HUMAN] [THRB_HUMAN] by SWISSPFAM
  • Domain found in 2A45: [Tryp_SPc ] by SMART
  • Other resources with information on 2A45
  • Community annotation for 2A45 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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