4WVB - JenaLib

Title :   CRYSTAL STRUCTURE OF GH63 MANNOSYLGLYCERATE HYDROLASE FROM THERMUS THERMOPHILUS HB8 IN COMPLEX WITH GLUCOSE

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

Date :   05 Nov 14 (Deposition) - 11 Mar 15 (Release) - 22 Apr 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.77

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (3x)
Biol. Unit 2: B  (3x)

Keywords :   Hydrolase, Gh63, (Alpha/Alpha)6-Barrel (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Miyazaki, M. Ichikawa, H. Iino, A. Nishikawa, T. Tonozuka
Crystal Structure And Substrate-Binding Mode Of Gh63 Mannosylglycerate Hydrolase From Thermus Thermophilus Hb8.
J. Struct. Biol. V. 190 21 2015
PubMed-ID: 25712767 | Reference-DOI: 10.1016/J.JSB.2015.02.006

Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-11A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	TTHA0978
	Organism Scientific	:	THERMUS THERMOPHILUS HB8
	Organism Taxid	:	300852

Structural Features

Chains, Units

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (3x)	:	A
Biological Unit 2 (3x)	:		B

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 7)

Asymmetric Unit (3, 7)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	GLC	1	Ligand/Ion	ALPHA-D-GLUCOSE
3	MPD	4	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Biological Unit 1 (2, 9)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GLC	3	Ligand/Ion	ALPHA-D-GLUCOSE
3	MPD	6	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Biological Unit 2 (1, 6)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GLC	-1	Ligand/Ion	ALPHA-D-GLUCOSE
3	MPD	6	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Sites (7, 7)

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:312 , GLN A:313 , HOH A:676	binding site for residue CL A 501
2	AC2	SOFTWARE	TYR A:113 , ARG A:243 , GLU A:280 , TRP A:360 , GLU A:364 , ARG A:420 , HOH A:623 , HOH A:714	binding site for residue MPD A 502
3	AC3	SOFTWARE	GLY A:100 , TRP A:141 , ALA A:145 , ARG A:146 , PHE A:214 , TYR A:219 , PRO A:221 , ILE A:224	binding site for residue MPD A 503
4	AC4	SOFTWARE	PRO A:23 , TRP A:32 , TRP A:34 , ASP A:35 , GLN A:103 , GLY A:163 , ASP A:165 , TYR A:349 , TRP A:350 , PHE A:408 , TRP A:410 , HOH A:768	binding site for residue GLC A 504
5	AC5	SOFTWARE	HIS B:312 , GLN B:313 , HOH B:703	binding site for residue CL B 500
6	AC6	SOFTWARE	TYR B:113 , ARG B:243 , ARG B:279 , GLU B:280 , TRP B:360 , GLU B:364 , ARG B:420 , HOH B:641 , HOH B:741	binding site for residue MPD B 501
7	AC7	SOFTWARE	GLY B:100 , TRP B:141 , ALA B:145 , ARG B:146 , TYR B:219 , PRO B:221 , ILE B:224	binding site for residue MPD B 502

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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:394
                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...............eehhhhhhhhhhhh..hhhhhhhhhhhhhhhhh........eee................eee.ee.......hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhh...hhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhee....ee..ee....ee....hhhhhhhhhhh..hhhhhhhhhhhhhhhhh..........................hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.eeee......eeeee.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wvb A   3 PLRTKAVEVLQRNSRGAFTVPAHGLYPYQWLWDSAFIALGWTQVDWERAWQELLCLFDYGQGPDGMLPHIVFHEQSRDYFPGPWGREARAQPATSGITQPPVVATVVRYLYEKDPDRDRARERARYLFPKLLAFHRWLYHARDPYRTGLVVIVHPWESGMDNSPAWDKPLSRVPVEDYDRYLSLLYLFRRLEYDPREIYRQSPFKVVDVGFNAILQRANRDLYALAVLLQEDPYEIEEWIVRGEVGLEALWDREAGFYFSWDLVAGEPIAVKTSAGFLPLFAGTPHQGRASLLAQEAERWGEKARYLLPSVDPTSPFFEPGRYWRGPVWINVNWMVAEGFRDYGFAALAARLKADALALMEREGFREYYDPLTGQGRGGEGFSWSAALALFWTR 420
                                    12        22        32        42        52        62        72        82  ||    94       104       114       124       134       144       154       164       174    || 206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416    
                                                                                                             85|                                                                                        179|                                                                                                                                                                                                                          
                                                                                                              88                                                                                         202

Chain B from PDB  Type:PROTEIN  Length:417
                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..............eehhhhhhhhhhhh..hhhhhhhhhhhhhhhhh........eee................eee.ee.......hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhh...hhhhhhhhhh.................hhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhee....ee..ee....ee....hhhhhhhhhhh..hhhhhhhhhhhhhhhhh..........................hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.eeee......eeeee.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wvb B   2 APLRTKAVEVLQRNSRGAFTVPAHGLYPYQWLWDSAFIALGWTQVDWERAWQELLCLFDYGQGPDGMLPHIVFHEQSRDYFPGPWGREARAQPATSGITQPPVVATVVRYLYEKDPDRDRARERARYLFPKLLAFHRWLYHARDPYRTGLVVIVHPWESGMDNSPAWDKPLSRVPVENLPPYERRDVKHVNPEERPRKEDYDRYLSLLYLFRRLEYDPREIYRQSPFKVVDVGFNAILQRANRDLYALAVLLQEDPYEIEEWIVRGEVGLEALWDREAGFYFSWDLVAGEPIAVKTSAGFLPLFAGTPHQGRASLLAQEAERWGEKARYLLPSVDPTSPFFEPGRYWRGPVWINVNWMVAEGFRDYGFAALAARLKADALALMEREGFREYYDPLTGQGRGGEGFSWSAALALFWTR 420
                                    11        21        31        41        51        61        71        81   ||   93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       
                                                                                                              85|                                                                                                                                                                                                                                                                                                                                            
                                                                                                               88

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 (5, 5)

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
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GLC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MPD	[ 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 ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Leu A:333 - Leu A:334	[ RasMol ]
		Leu B:333 - Leu B:334	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ 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 \| Biol. Unit 2 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
	4wvb
		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
	Q5SJN0_THET8 \| Q5SJN0
		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)
	(no 'Enzyme Classificator' available)
		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
	Q5SJN0_THET8 \| Q5SJN0
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description