Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE 6-PHOSPHOGLUCONOLACTONASE (YP_574786.1) FROM CHROMOHALOBACTER SALEXIGENS DSM 3043 AT 1.88 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  23 Feb 10  (Deposition) - 07 Apr 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Putative 6-Phosphogluconolactonase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative 6-Phosphogluconolactonase (Yp_574786. 1) From Chromohalobacter Salexigens Dsm 3043 At 1. 88 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 6-PHOSPHOGLUCONOLACTONASE
    Chains: A
    EC Number: 3.1.1.31
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CSAL_2740
    Organism Scientific: CHROMOHALOBACTER SALEXIGENS
    Organism Taxid: 290398
    Strain: DSM 3043 / ATCC BAA-138 / NCIMB 13768

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE1Mod. Amino AcidSELENOMETHIONINE
3NA1Ligand/IonSODIUM ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MSE2Mod. Amino AcidSELENOMETHIONINE
3NA-1Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:180 , ALA A:181BINDING SITE FOR RESIDUE GOL A 226
2AC2SOFTWARETRP A:70 , VAL A:71 , THR A:101 , THR A:102 , ASP A:103 , ASP A:104 , HOH A:245BINDING SITE FOR RESIDUE GOL A 227
3AC3SOFTWAREALA A:163 , VAL A:166 , HOH A:288 , HOH A:335 , HOH A:374 , HOH A:377BINDING SITE FOR RESIDUE NA A 228

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LWD)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Trp A:123 -Pro A:124

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LWD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LWD)

(-) Exons   (0, 0)

(no "Exon" information available for 3LWD)

(-) 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:223
 aligned with Q1QTX1_CHRSD | Q1QTX1 from UniProtKB/TrEMBL  Length:225

    Alignment length:223
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222   
         Q1QTX1_CHRSD     3 NTTQEGRQRLAERLADTVAQALEADLAKRERALLVVSGGSTPKPFFTSLAAKALPWARVDVTLADERWVTADDADSNARLVRETLLVGPAAEACFHPLTTDDDTPEAGVETVAERLESLPWPASAVILGMGGDGHTASLFPDSEQLATALETTSAAVVVHAPSVPQARITLSASRLADAGLHVLHITGNDKRRVLAEALAGDDVRQLPIRAFLSQPIATYWAP 225
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------Glucosamine_iso-3lwdA01 A:12-202                                                                                                                                                               ----------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhh...hhh.eeeee.eee........hhhhhhhhhh.hhhhhhheee.......hhhhhhhhhhhhhhh......eeee................hhhhhhhh...eeee........eeeehhhhhh....eeeeeehhhhhhhhhhhhhh.......hhhhhh...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lwd A   3 NTTQEGRQRLAERLADTVAQALEADLAKRERALLVVSGGSTPKPFFTSLAAKALPWARVDVTLADERWVTADDADSNARLVRETLLVGPAAEACFHPLTTDDDTPEAGVETVAERLESLPWPASAVILGmGGDGHTASLFPDSEQLATALETTSAAVVVHAPSVPQARITLSASRLADAGLHVLHITGNDKRRVLAEALAGDDVRQLPIRAFLSQPIATYWAP 225
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222   
                                                                                                                                                           132-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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3LWD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LWD)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: ISOCOT_Fold (53)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q1QTX1_CHRSD | Q1QTX1)
molecular function
    GO:0017057    6-phosphogluconolactonase activity    Catalysis of the reaction: 6-O-phosphono-D-glucono-1,5-lactone + H(2)O = 6-phospho-D-gluconate + H(+).
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0006098    pentose-phosphate shunt    The glucose-6-phosphate catabolic process in which, coupled to NADPH synthesis, glucose-6-P is oxidized with the formation of carbon dioxide (CO2) and ribulose 5-phosphate; ribulose 5-P then enters a series of reactions interconverting sugar phosphates. The pentose phosphate pathway is a major source of reducing equivalents for biosynthesis reactions and is also important for the conversion of hexoses to pentoses.

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Trp A:123 - Pro A:124   [ 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
  3lwd
    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
  Q1QTX1_CHRSD | Q1QTX1
    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)
  3.1.1.31
    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
  Q1QTX1_CHRSD | Q1QTX1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 3LWD)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3LWD)