3NDH	Hydrolase Dna	date	Jun 07, 2010
title	Restriction Endonuclease In Complex With Substrate Dna
authors	M.Firczuk, M.Wojciechowski, H.Czapinska, M.Bochtler
compound		source
Molecule: Restriction Endonuclease Thai Chain: A, B Synonym: Putative Uncharacterized Protein Ta0828 Engineered: Yes		Organism_scientific: Thermoplasma Acidophilum Organism_taxid: 2303 Strain: Atcc25905 Gene: Ta0828 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Er2566 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet15bmod
Molecule: Dna (5'-D(Ggptpapcpgpcpgpaptpg)-3') Chain: C Engineered: Yes		Synthetic: Yes
Molecule: Dna (5'-D(Ccpaptpcpgpcpgptpapc)-3') Chain: D Engineered: Yes		Synthetic: Yes
symmetry	Space Group: P 1 21 1	R_factor 0.172 R_Free 0.183
crystal cell	length a length b length c angle alpha angle beta angle gamma 39.310 72.910 88.760 90.00 101.99 90.00
method	X-Ray Diffraction	resolution	1.30 Å
ligand	ACT, CL, NA, PGE, SO4	enzyme
note	3NDH is a representative structure
Primary reference	DNA intercalation without flipping in the specific ThaI-DNA complex., Firczuk M, Wojciechowski M, Czapinska H, Bochtler M, Nucleic Acids Res. 2011 Jan 1;39(2):744-54. Epub 2010 Sep 21. PMID:20861000

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (209 Kb) [Save to disk] Biological Unit Coordinates (3ndh.pdb1.gz) 202 Kb LPC: Ligand-Protein Contacts for 3NDH CSU: Contacts of Structural Units for 3NDH Structure Factors (824 Kb) Retrieve 3NDH in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3NDH from S2C, [Save to disk] Re-refined 3ndh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3NDH 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 3NDH

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 3NDH, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3ndh_D] [3ndh_B] [3ndh_C] [3ndh] [3ndh_A] SWISS-PROT database: Domain organization of by SWISSPFAM

Other resources with information on 3NDH

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

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