1JIB	Hydrolase	date	Jul 02, 2001
title	Complex Of Alpha-Amylase II (Tva II) From Thermoactinomyces R-47 With Maltotetraose Based On A Crystal Soaked With Malt
authors	T.Yokota, T.Tonozuka, Y.Shimura, K.Ichikawa, S.Kamitori, Y.Sakano
compound		source
Molecule: Neopullulanase Chain: A, B Ec: 3.2.1.135 Engineered: Yes Mutation: Yes		Organism_scientific: Thermoactinomyces Vulgaris Organism_taxid: 2026 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Mv1184 Expression_system_vector_type: Plasmid Expression_system_plasmid: Ptnd325n
symmetry	Space Group: P 21 21 21	R_factor 0.212 R_Free 0.304
crystal cell	length a length b length c angle alpha angle beta angle gamma 111.870 117.320 112.610 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	3.30 Å
ligand	GLC	enzyme	Hydrolase E.C.3.2.1.135 BRENDA
Gene Ontology	Chain Function Process Component A, B
Primary reference	Structures of Thermoactinomyces vulgaris R-47 alpha-amylase II complexed with substrate analogues., Yokota T, Tonozuka T, Shimura Y, Ichikawa K, Kamitori S, Sakano Y, Biosci Biotechnol Biochem 2001 Mar;65(3):619-26. PMID:11330677

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (195 Kb) [Save to disk] Biological Unit Coordinates (1jib.pdb1.gz) 96 Kb Biological Unit Coordinates (1jib.pdb2.gz) 97 Kb LPC: Ligand-Protein Contacts for 1JIB CSU: Contacts of Structural Units for 1JIB Likely Quarternary Molecular Structure file(s) for 1JIB Structure Factors (244 Kb) Retrieve 1JIB in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1JIB from S2C, [Save to disk] Re-refined 1jib structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1JIB 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 1JIB

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 1JIB, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1jiba1, region A:1-120 [Jmol] [rasmolscript] [script source]     - Domain d1jiba3, region A:121-502 [Jmol] [rasmolscript] [script source]     - Domain d1jiba2, region A:503-585 [Jmol] [rasmolscript] [script source]     - Domain d1jibb1, region B:1-120 [Jmol] [rasmolscript] [script source]     - Domain d1jibb3, region B:121-502 [Jmol] [rasmolscript] [script source]     - Domain d1jibb2, region B:503-585 [Jmol] [rasmolscript] [script source] 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: [1jib_B] [1jib_A] [1jib] SWISS-PROT database: [Q08751] Domain organization of [NEPU2_THEVU] by SWISSPFAM Domain found in 1JIB: [Aamy ] by SMART

Other resources with information on 1JIB

Community annotation for 1JIB at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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