4XPO - JenaLib

Title :   CRYSTAL STRUCTURE OF A NOVEL ALPHA-GALACTOSIDASE FROM PEDOBACTER SALTANS

Authors :   T. Miyazaki, Y. Ishizaki, M. Ichikawa, A. Nishikawa, T. Tonozuka

Date :   17 Jan 15 (Deposition) - 20 May 15 (Release) - 09 Sep 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Hydrolase, Tim-Barrel, Gh31 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Miyazaki, Y. Ishizaki, M. Ichikawa, A. Nishikawa, T. Tonozuka
Structural And Biochemical Characterization Of Novel Bacterial Alpha-Galactosidases Belonging To Glycoside Hydrolase Family 31
Biochem. J. V. 469 145 2015
PubMed-ID: 25942325 | Reference-DOI: 10.1042/BJ20150261

Compounds

Molecule 1 - ALPHA-GLUCOSIDASE
	Chains	:	A
	EC Number	:	3.2.1.22
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	PEDOBACTER SALTANS
	Organism Taxid	:	151895
	Strain	:	NBRC 100064

Structural Features

Chains, Units

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 5)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
2	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 1 (2, 10)

No.	Name	Count	Type	Full Name
1	EDO	8	Ligand/Ion	1,2-ETHANEDIOL
2	TRS	2	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:266 , TRP A:305 , LYS A:363 , ASP A:365 , GLU A:366 , ASP A:434 , ASN A:484 , TRP A:486 , HOH A:1116 , HOH A:1249 , HOH A:1377	binding site for residue TRS A 1001
2	AC2	SOFTWARE	TYR A:100 , PHE A:450 , GLY A:533 , MET A:534 , ILE A:567 , HOH A:1202	binding site for residue EDO A 1002
3	AC3	SOFTWARE	TYR A:515 , ALA A:519 , ARG A:522 , ASP A:575 , ASP A:576 , HOH A:1122	binding site for residue EDO A 1003
4	AC4	SOFTWARE	HIS A:122 , TYR A:373 , ARG A:418 , ASP A:434 , HOH A:1258	binding site for residue EDO A 1004
5	AC5	SOFTWARE	PHE A:601 , ARG A:653 , TYR A:655 , HOH A:1277 , HOH A:1432	binding site for residue EDO A 1005

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:665
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeeeee.....hhhhhhh...hhhhhhh.............eeeee..eeeeeee......eee............eeeeeee.........ee.....eeee...eeeeee....eeeee..............................eeeeee...eeeeeee...hhhhhhhhhhhhh......hhhhh.eeee.....hhhhhhhhhhhhhhhh....eeeehhhhh................hhhhhhhhhhhh..eeeeee.........hhhhhhhhh..............hhhhhhhhhhhhhhhhhhhh..eeee.....................hhhhhhhhhhhhhhhhhhhhhhhh.....eee...........eee.....hhhhhhhhhhhhh....ee........hhhhhhhhhhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee............eee...eee.........eeee....eeee.....eeee..eeee........eeee...eeee.............eeeeeee.....eeeeeee.....hhhhhh..eeeeeeeee.....eeeee..........eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xpo A  29 NWTEIYPGVWKATVGKPESYDLLKAAGAQPNKDALSKTEKVSFPFANGGVSLEVSGGKTYLRFPLQKEEQLYGFGLNFQTVHQRGKILELHVDHYGGKDSGRTHAPTPFYVSSNGYGVFINSARYIKVWAGTGVRKDSENFPTPKDRNTDKTWSSRPYSDAVEILVPAEGVEVYVFGGPKPIDAVKRYNLLNGGGYLPPRWGLGFTQRVMTRYTDKDVEKEVNDFKEKGYPLDFVGLEPGWQSKAYPGTFSWDKSRYPDPTSFVKKMKDQGIRLNLWINPYISPDAPFYKEIKPYTGSHTVWLGLVPDFTMAEARKPFFNQLLKDQIERGVSGYKIDEVDGYDYYLWPDAAKFPSGLSAEQMRQTYGLLVQRYSAELYKQRNERTFGLVRASNGGGTSFPYVIYNDYYNHQDFITALINSGFAGVLWTPEVRASKSGEEWLRRFQSNVFSPMAMINAWASGTKPWSYPEVEADVKKFALLRMQMMPYWYSAFARYHFEGMPPFRGMGLESKEIKDQYMAGDDLLVAPMFAGEKSRKVVLPKGKWYDFYTGEYAGDGEVLDVTPGLDKIPVYVRDGGIVPMMPALLNSPKSNQKVDLEIRYYGNKPGEFKLYDDDGETFNYEKGDFSWRTIRVEKDKSGKVKGSISAAVKGKVNTVGKVTFTAMTK 719
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      537|                                                                                                                                                           
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       564

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

Visualization

Interactive Views

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		TRS	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly A:206 - Pro A:207	[ RasMol ]
		Gly A:369 - Tyr A:370	[ RasMol ]
		Tyr A:274 - Pro A:275	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	4xpo
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	A0A0F7R6D6_9 \| A0A0F7R6D6
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	3.2.1.22
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	A0A0F7R6D6_9 \| A0A0F7R6D6
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File

4xpp	THE SAME PROTEIN COMPLEXED WITH D-GALACTOSE
4xpq	THE SAME PROTEIN COMPLEXED WITH L-FUCOSE
4xpr	THE MUTANT D365A
4xps	THE MUTANT D365A COMPLEXED WITH P-NITROPHENYL-ALPHA-D- GALACTOPYRANOSIDE

Description