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 Diffractionresolution 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
ChainFunctionProcessComponent
A, C


D, B


Primary referenceCrystal 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
  • 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 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]
  • Fold representative 1rd3 from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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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