2QW5 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A PUTATIVE SUGAR PHOSPHATE ISOMERASE/EPIMERASE (AVA4194) FROM ANABAENA VARIABILIS ATCC 29413 AT 1.78 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   09 Aug 07 (Deposition) - 04 Sep 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.78

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

Keywords :   Putative Sugar Phosphate Isomerase/Epimerase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Sugar Phosphate Isomerase/Epimerase (Yp_324688. 1) From Anabaena Variabilis Atcc 29413 At 1. 78 A Resolution
To Be Published
PubMed: search

Molecule 1 - XYLOSE ISOMERASE-LIKE TIM BARREL
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	SPEEDET
	Expression System Strain	:	HK100
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	YP_324688.1, AVA_4194
	Organism Scientific	:	ANABAENA VARIABILIS ATCC 29413
	Organism Taxid	:	240292
	Strain	:	PCC 7937

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 16)

No.	Name	Count	Type	Full Name
1	CL	5	Ligand/Ion	CHLORIDE ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
4	XLS	2	Ligand/Ion	D-XYLOSE (LINEAR FORM)
5	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (3, 18)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	2	Ligand/Ion	GLYCEROL
3	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
4	XLS	4	Ligand/Ion	D-XYLOSE (LINEAR FORM)
5	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (3, 10)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	2	Ligand/Ion	GLYCEROL
3	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
4	XLS	2	Ligand/Ion	D-XYLOSE (LINEAR FORM)
5	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (2, 8)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	-1	Ligand/Ion	GLYCEROL
3	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
4	XLS	2	Ligand/Ion	D-XYLOSE (LINEAR FORM)
5	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:86 , PRO A:128 , GLU A:182 , GLU A:188 , HIS A:218 , ARG A:252 , PHE A:282 , HOH A:406 , HOH A:530	BINDING SITE FOR RESIDUE XLS A 401
02	AC2	SOFTWARE	ASN B:86 , PRO B:128 , GLU B:182 , GLU B:188 , HIS B:218 , ARG B:252 , PHE B:282 , HOH B:404 , HOH B:537	BINDING SITE FOR RESIDUE XLS B 401
03	AC3	SOFTWARE	GLU A:182 , ASP A:215 , GLN A:246 , ARG A:252 , GLU A:280 , HOH A:406	BINDING SITE FOR RESIDUE ZN A 400
04	AC4	SOFTWARE	GLU B:182 , ASP B:215 , GLN B:246 , GLU B:280 , HOH B:404	BINDING SITE FOR RESIDUE ZN B 400
05	AC5	SOFTWARE	ALA A:287 , HOH A:510	BINDING SITE FOR RESIDUE CL A 402
06	AC6	SOFTWARE	PRO B:286 , ALA B:287 , HOH B:445	BINDING SITE FOR RESIDUE CL B 402
07	AC7	SOFTWARE	PRO A:100 , GLU A:101 , PRO B:100 , GLU B:101	BINDING SITE FOR RESIDUE CL A 403
08	AC8	SOFTWARE	ARG B:103 , GLN B:104 , HOH B:750	BINDING SITE FOR RESIDUE CL B 403
09	AC9	SOFTWARE	ARG A:103 , GLN A:104	BINDING SITE FOR RESIDUE CL A 404
10	BC1	SOFTWARE	ASP A:315 , GLU B:101 , GLN B:104 , GLU B:108 , HOH B:661	BINDING SITE FOR RESIDUE GOL A 405

(no "SS Bond" information available for 2QW5)

Asymmetric Unit

No.	Residues
1	Gly A:191	-	Pro A:192
2	Gly B:191	-	Pro B:192

(no "SAP(SNP)/Variant" information available for 2QW5)

(no "PROSITE Motif" information available for 2QW5)

(no "Exon" information available for 2QW5)

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:327
 aligned with Q3M5E3_ANAVT | Q3M5E3 from UniProtKB/TrEMBL  Length:334

    Alignment length:327
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       
         Q3M5E3_ANAVT     6 ATSDIYISFFMFTTNLQPDNLDYRRIVVAHIKKLQRFGYSGFEFPIAPGLPENYAQDLENYTNLRHYLDSEGLENVKISTNVGATRTFDPSSNYPEQRQEALEYLKSRVDITAALGGEIMMGPIVIPYGVFPTTDFNEPIWSDELQEHLKVRYANAQPILDKLGEYAEIKKVKLAIEPITHWETPGPNKLSQLIEFLKGVKSKQVGVVIDSAHEILDGEGPEIFKTQVEYLAQQGRLHYVQVSPPDRGALHTSWLPWKSFLTPIVKVYDGPIAVEIFNAIPAFTNSLRLTRRKFWIPDEDPPNQYPNAYDIADEAIKVTRKELKKIG 332
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qw5A00 A:6-332 Divalent-metal-dependent TIM barrel enzymes                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.hhh.......hhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhhhhhh.....eeeee............hhhhhhhhhhhhhhhhhhhhhh...eeee..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee............hhhhhhhhhh......eeeeeehhhhhhhh.hhhhhhhhhhhhhhhh.eeeeee.............hhhhhhhhhhhhh...eee.....hhhhhh.....................hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qw5 A   6 ATSDIYISFFmFTTNLQPDNLDYRRIVVAHIKKLQRFGYSGFEFPIAPGLPENYAQDLENYTNLRHYLDSEGLENVKISTNVGATRTFDPSSNYPEQRQEALEYLKSRVDITAALGGEImmGPIVIPYGVFPTTDFNEPIWSDELQEHLKVRYANAQPILDKLGEYAEIKKVKLAIEPITHWETPGPNKLSQLIEFLKGVKSKQVGVVIDSAHEILDGEGPEIFKTQVEYLAQQGRLHYVQVSPPDRGALHTSWLPWKSFLTPIVKVYDGPIAVEIFNAIPAFTNSLRLTRRKFWIPDEDPPNQYPNAYDIADEAIKVTRKELKKIG 332
                                    15|       25        35        45        55        65        75        85        95       105       115       125|      135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       
                                     16-MSE                                                                                                      125-MSE                                                                                                                                                                                                           
                                                                                                                                                  126-MSE

Chain B from PDB  Type:PROTEIN  Length:325
 aligned with Q3M5E3_ANAVT | Q3M5E3 from UniProtKB/TrEMBL  Length:334

    Alignment length:325
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327     
         Q3M5E3_ANAVT     8 SDIYISFFMFTTNLQPDNLDYRRIVVAHIKKLQRFGYSGFEFPIAPGLPENYAQDLENYTNLRHYLDSEGLENVKISTNVGATRTFDPSSNYPEQRQEALEYLKSRVDITAALGGEIMMGPIVIPYGVFPTTDFNEPIWSDELQEHLKVRYANAQPILDKLGEYAEIKKVKLAIEPITHWETPGPNKLSQLIEFLKGVKSKQVGVVIDSAHEILDGEGPEIFKTQVEYLAQQGRLHYVQVSPPDRGALHTSWLPWKSFLTPIVKVYDGPIAVEIFNAIPAFTNSLRLTRRKFWIPDEDPPNQYPNAYDIADEAIKVTRKELKKIG 332
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qw5B00 B:8-332 Divalent-metal-dependent TIM barrel enzymes                                                                                                                                                                                                                                                                           CATH domains
           Pfam domains (1) ----------------------------AP_endonuc_2-2qw5B01 B:36-257                                                                                                                                                                                                 --------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------AP_endonuc_2-2qw5B02 B:36-257                                                                                                                                                                                                 --------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..eeee.hhh.......hhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhhhhhh.....eeeee............hhhhhhhhhhhhhhhhhhhhhh...eeee..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee............hhhhhhhhhhh.....eeeeeehhhhhhhh.hhhhhhhhhhhhhhh..eeeeee.............hhhhhhhhhhhhh...eee.....hhhhhh.....................hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qw5 B   8 SDIYISFFmFTTNLQPDNLDYRRIVVAHIKKLQRFGYSGFEFPIAPGLPENYAQDLENYTNLRHYLDSEGLENVKISTNVGATRTFDPSSNYPEQRQEALEYLKSRVDITAALGGEImmGPIVIPYGVFPTTDFNEPIWSDELQEHLKVRYANAQPILDKLGEYAEIKKVKLAIEPITHWETPGPNKLSQLIEFLKGVKSKQVGVVIDSAHEILDGEGPEIFKTQVEYLAQQGRLHYVQVSPPDRGALHTSWLPWKSFLTPIVKVYDGPIAVEIFNAIPAFTNSLRLTRRKFWIPDEDPPNQYPNAYDIADEAIKVTRKELKKIG 332
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327     
                                   16-MSE                                                                                                      125-MSE                                                                                                                                                                                                           
                                                                                                                                                126-MSE

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 '\|'

(no "SCOP Domain" information available for 2QW5)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Divalent-metal-dependent TIM barrel enzymes (98)

Anabaena variabilis atcc 29413. Organism_taxid: 240292. Strain: pcc 7937. (1)

1a	2qw5A00	A:6-332
1b	2qw5B00	B:8-332

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: AP_endonuc_2 (72)

Anabaena variabilis (strain ATCC 29413 / PCC 7937) (1)

1a	AP_endonuc_2-2qw5B01	B:36-257
1b	AP_endonuc_2-2qw5B02	B:36-257

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q3M5E3_ANAVT | Q3M5E3)

molecular function
	GO:0016853		isomerase activity		Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	GO:0046872		metal ion binding		Interacting selectively and non-covalently with any metal ion.

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 ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		XLS	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ 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 ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly A:191 - Pro A:192	[ RasMol ]
		Gly B:191 - Pro B:192	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

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 \| Biol. Unit 3 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)

Access by PDB/NDB ID
	2qw5
		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
	Q3M5E3_ANAVT \| Q3M5E3
		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

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
	Q3M5E3_ANAVT \| Q3M5E3
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 2QW5)

(no "Related Entries Specified in the PDB File" available for 2QW5)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 16)

Sites (10, 10)

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

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (2, 2)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File