2D0G	Hydrolase	date	Aug 02, 2005
title	Crystal Structure Of Thermoactinomyces Vulgaris R-47 Alpha-A (Tvai) Mutant D356ne396q Complexed With P5, A Pullulan Mod Oligosaccharide
authors	A.Abe, H.Yoshida, T.Tonozuka, Y.Sakano, S.Kamitori
compound		source
Molecule: Alpha-Amylase I Chain: A Synonym: Tva I Ec: 3.2.1.1 Engineered: Yes Mutation: Yes		Organism_scientific: Thermoactinomyces Vulgaris Organism_taxid: 2026 Strain: R-47 Expression_system: Escherichia Coli Expression_system_taxid: 562
symmetry	Space Group: C 1 2 1	R_factor 0.150 R_Free 0.190
crystal cell	length a length b length c angle alpha angle beta angle gamma 120.885 50.698 108.007 90.00 103.43 90.00
method	X-Ray Diffraction	resolution	2.60 Å
ligand	BGC, CA, GLC, MPD	enzyme	Hydrolase E.C.3.2.1.1 BRENDA
Gene Ontology	Chain Function Process Component A
Primary reference	Complexes of Thermoactinomyces vulgaris R-47 alpha-amylase 1 and pullulan model oligossacharides provide new insight into the mechanism for recognizing substrates with alpha-(1,6) glycosidic linkages., Abe A, Yoshida H, Tonozuka T, Sakano Y, Kamitori S, FEBS J. 2005 Dec;272(23):6145-53. PMID:16302977

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (121 Kb) [Save to disk] Biological Unit Coordinates (2d0g.pdb1.gz) 112 Kb LPC: Ligand-Protein Contacts for 2D0G CSU: Contacts of Structural Units for 2D0G Likely Quarternary Molecular Structure file(s) for 2D0G Structure Factors (167 Kb) Retrieve 2D0G in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2D0G from S2C, [Save to disk] Re-refined 2d0g structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2D0G 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 2D0G

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 2D0G, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2d0g] [2d0g_A] SWISS-PROT database: [Q60053] Domain organization of [NEPU1_THEVU] by SWISSPFAM Domains found in 2D0G: [Aamy] [Aamy_C ] by SMART

Other resources with information on 2D0G

Community annotation for 2D0G at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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