3DD2	Hydrolase Hydrolase Inhibitor Rna	date	Jun 04, 2008
title	Crystal Structure Of An Rna Aptamer Bound To Human Thrombin
authors	S.B.Long, B.A.Sullenger
compound		source
Molecule: Thrombin Light Chain Chain: L		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606
Molecule: Thrombin Heavy Chain Chain: H Ec: 3.4.21.5		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606
Molecule: Rna (26-Mer) Chain: B Engineered: Yes		Synthetic: Yes
symmetry	Space Group: P 21 21 2	R_factor 0.204 R_Free 0.254
crystal cell	length a length b length c angle alpha angle beta angle gamma 83.766 134.017 44.033 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.90 Å
ligand	0G6, ACY, CFL, MG, P6G, PEG, UFT	enzyme	Hydrolase E.C.3.4.21.5 BRENDA
Gene Ontology	Chain Function Process Component H L
Primary reference	Crystal structure of an RNA aptamer bound to thrombin., Long SB, Long MB, White RR, Sullenger BA, RNA. 2008 Oct 29. PMID:18971322

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (72 Kb) [Save to disk] Biological Unit Coordinates (3dd2.pdb1.gz) 65 Kb LPC: Ligand-Protein Contacts for 3DD2 CSU: Contacts of Structural Units for 3DD2 Likely Quarternary Molecular Structure file(s) for 3DD2 Structure Factors (295 Kb) Retrieve 3DD2 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3DD2 from S2C, [Save to disk] Re-refined 3dd2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3DD2 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 3DD2

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 3DD2, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1m3dd2, region D:115-228 [Jmol] [rasmolscript] [script source]

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3dd2_B] [3dd2] [3dd2_L] [3dd2_H] SWISS-PROT database: [P00734] Domain organization of [THRB_HUMAN] by SWISSPFAM Domain found in 3DD2: [Tryp_SPc ] by SMART

Other resources with information on 3DD2

Community annotation for 3DD2 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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