2ODY	Blood Clotting Blood Clotting Inhibitor	date	Dec 27, 2006
title	Thrombin-Bound Boophilin Displays A Functional And Accessibl Reactive-Site Loop
authors	S.Macedo-Ribeiro, P.Fuentes-Prior, P.J.B.Pereira
compound		source
Molecule: Prothrombin (Ec 3.4.21.5) Chain: A, C Fragment: Thrombin Light Chain, Residues 318-366 Synonym: Coagulation Factor II Ec: 3.4.21.5		Organism_scientific: Bos Taurus Organism_common: Cattle Organism_taxid: 9913
Molecule: Prothrombin (Ec 3.4.21.5) Chain: B, D Fragment: Thrombin Heavy Chain, Residues 367-625 Synonym: Coagulation Factor II Ec: 3.4.21.5		Organism_scientific: Bos Taurus Organism_common: Cattle Organism_taxid: 9913
Molecule: Boophilin Chain: E, F Fragment: Boophilin (Isoform H2), Residues 16-142 Engineered: Yes		Organism_scientific: Rhipicephalus Microplus Organism_common: Southern Cattle Tick Organism_taxid: 6941 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Dh5alpha Expression_system_vector_type: Plasmid
symmetry	Space Group: P 21 21 21	R_factor 0.190 R_Free 0.230
crystal cell	length a length b length c angle alpha angle beta angle gamma 92.500 104.200 129.100 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.35 Å
ligand	NA, NAG, PO4	enzyme	Hydrolase E.C.3.4.21.5 BRENDA
Gene Ontology	Chain Function Process Component A, C D, B F, E serine-type endopeptidase in...
Primary reference	Isolation, cloning and structural characterisation of boophilin, a multifunctional kunitz-type proteinase inhibitor from the cattle tick., Macedo-Ribeiro S, Almeida C, Calisto BM, Friedrich T, Mentele R, Sturzebecher J, Fuentes-Prior P, Pereira PJ, PLoS ONE. 2008 Feb 20;3(2):e1624. PMID:18286181

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (150 Kb) [Save to disk] Biological Unit Coordinates (2ody.pdb1.gz) 73 Kb Biological Unit Coordinates (2ody.pdb2.gz) 73 Kb LPC: Ligand-Protein Contacts for 2ODY CSU: Contacts of Structural Units for 2ODY Likely Quarternary Molecular Structure file(s) for 2ODY Structure Factors (784 Kb) Retrieve 2ODY in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2ODY from S2C, [Save to disk] Re-refined 2ody structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2ODY in 3D

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Visual 3D analysis of 2ODY

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 3D motif for 2ODY, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2ody] [2ody_A] [2ody_C] [2ody_E] [2ody_F] [2ody_D] [2ody_B] SWISS-PROT database: [Q8WPI2] [P00735] Domain organization of [Q8WPI2_BOOMI] [THRB_BOVIN] by SWISSPFAM Domains found in 2ODY: [KU] [Tryp_SPc ] by SMART

Other resources with information on 2ODY

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

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