6EO7	Hydrolase Dna	date	Oct 09, 2017
title	X-Ray Structure Of The Complex Between Human Alpha-Thrombin Modified 15-Mer Dna Aptamer Containing 5-(3-(Acetamide-N-Yl Propen-1-Yl)-2'-Deoxyuridine Residue
authors	R.M.Dolot, B.Nawrot, X.Yang
compound		source
Molecule: Ga68b2 - Modified Human Thrombin Binding Aptamer Chain: D Engineered: Yes Other_details: Thrombin-Specific 15-Mer Dna Aptamer Contain (Acetamide-N-Yl)-1-Propen-1-Yl)-2'-Deoxyuridine Residue;		Synthetic: Yes Organism_scientific: Synthetic Construct Organism_taxid: 32630
Molecule: Prothrombin Chain: L Synonym: Coagulation Factor II Ec: 3.4.21.5		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606
Molecule: Prothrombin Chain: H Synonym: Coagulation Factor II Ec: 3.4.21.5		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606
symmetry	Space Group: P 32 2 1	R_factor 0.161 R_Free 0.208
crystal cell	length a length b length c angle alpha angle beta angle gamma 94.579 94.579 125.566 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.24 Å
ligand	0G6, 8DT, K, NA, NAG	enzyme	Hydrolase E.C.3.4.21.5 BRENDA
Gene Ontology	Chain Function Process Component H L
Primary reference	Crystal structures of thrombin in complex with chemically modified thrombin DNA aptamers reveal the origins of enhanced affinity., Dolot R, Lam CH, Sierant M, Zhao Q, Liu FW, Nawrot B, Egli M, Yang X, Nucleic Acids Res. 2018 May 18;46(9):4819-4830. doi: 10.1093/nar/gky268. PMID:29684204

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (68 Kb) [Save to disk] Biological Unit Coordinates (6eo7.pdb1.gz) 61 Kb LPC: Ligand-Protein Contacts for 6EO7 CSU: Contacts of Structural Units for 6EO7 Structure Factors (892 Kb) Retrieve 6EO7 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 6EO7 from S2C, [Save to disk]

View 6EO7 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 6EO7

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

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [6eo7_L] [6eo7_D] [6eo7_H] SWISS-PROT database: Domain organization of by SWISSPFAM

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