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 Diffraction	resolution	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	Chain Function Process Component H, K eukaryotic cell surface bind... chaperone binding platelet degranulation blood coagulation hemostasis platelet activation response to calcium ion extracellular region fibrinogen complex extracellular space plasma membrane cell cortex external side of plasma memb... platelet alpha granule platelet alpha granule lumen... blood microparticle I, L eukaryotic cell surface bind... metal ion binding platelet degranulation blood coagulation hemostasis platelet activation response to calcium ion extracellular region fibrinogen complex extracellular space plasma membrane cell cortex external side of plasma memb... platelet alpha granule platelet alpha granule lumen... blood microparticle
Primary reference	Structural 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

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_A] [2a45_B] [2a45_C] [2a45_D] [2a45_E] [2a45_F] [2a45_H] [2a45_I] [2a45_K] [2a45_L] [2a45_G] [2a45_J] 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 Alignments of the sequence of 2A45 with the sequences similar proteins can be viewed for 2A45's classification [FIBA_HUMAN] [FIBB_HUMAN] [FIBG_HUMAN] [THRB_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_HUMAN] [FIBG_HUMAN] [THRB_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 2A45

Community annotation for 2A45 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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