1RD3	Hydrolase	date	Nov 05, 2003
title	2.5a Structure Of Anticoagulant Thrombin Variant E217k
authors	W.J.Carter, T.Myles, L.L.Leung, J.A.Huntington
compound		source
Molecule: Prothrombin Chain: A, C Fragment: Thrombin Light Chain Synonym: Coagulation Factor II Ec: 3.4.21.5 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: F2 Expression_system: Cricetinae Gen. Sp. Expression_system_taxid: 36483 Expression_system_strain: Bhk-21
Molecule: Prothrombin Chain: B, D Fragment: Thrombin Heavy Chain Synonym: Coagulation Factor II Ec: 3.4.21.5 Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: F2 Expression_system: Cricetinae Gen. Sp. Expression_system_taxid: 36483 Expression_system_strain: Bhk-21
symmetry	Space Group: P 21 21 21	R_factor 0.229 R_Free 0.259
crystal cell	length a length b length c angle alpha angle beta angle gamma 73.230 107.620 136.030 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.50 Å
ligand	BMA, FUC, GOL, MAN, NAG, NDG, PO4	enzyme	Hydrolase E.C.3.4.21.5 BRENDA
related structures	by homologous chain: 1AVG, 1BMM, 1TB6, 1UVT
Gene Ontology	Chain Function Process Component A, C D, B
Primary reference	Crystal structure of anticoagulant thrombin variant E217K provides insights into thrombin allostery., Carter WJ, Myles T, Gibbs CS, Leung LL, Huntington JA, J Biol Chem 2004 Apr 9;. PMID:15075325

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (103 Kb) [Save to disk] Biological Unit Coordinates (1rd3.pdb1.gz) 97 Kb Biological Unit Coordinates (1rd3.pdb2.gz) 51 Kb Biological Unit Coordinates (1rd3.pdb3.gz) 49 Kb LPC: Ligand-Protein Contacts for 1RD3 CSU: Contacts of Structural Units for 1RD3 Likely Quarternary Molecular Structure file(s) for 1RD3 Structure Factors (289 Kb) Retrieve 1RD3 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1RD3 from S2C, [Save to disk] Re-refined 1rd3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1RD3 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 1RD3

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 1RD3, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1rd3.1, region A:,B [Jmol] [rasmolscript] [script source]     - Domain d1rd3.2, region C:,D [Jmol] [rasmolscript] [script source]     - Domain d1e1rd3, region D:82-357 [Jmol] [rasmolscript] [script source] Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH Summaries and structural analyses of PDB data files from PDBSum Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1rd3_A] [1rd3_D] [1rd3_C] [1rd3_B] [1rd3] SWISS-PROT database: [P00734] Domain organization of [THRB_HUMAN] by SWISSPFAM Domain found in 1RD3: [Tryp_SPc ] by SMART

Other resources with information on 1RD3

Community annotation for 1RD3 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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