Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF MANNOSE-6-PHOSPHATE ISOMERASE FROM HELICOBACTER PYLORI
 
Authors :  Y. Patskovsky, U. Ramagopal, R. Toro, J. M. Sauder, M. Dickey, M. Iizuka M. Maletic, S. R. Wasserman, J. Koss, S. K. Burley, S. C. Almo, New York Research Center For Structural Genomics (Nysgxrc)
Date :  29 Jun 07  (Deposition) - 17 Jul 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Isomerase, Structural Genomics, Psi, Protein Structure Initiative, Nysgrc, New York Structural Genomics Research Consortium, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, U. Ramagopal, R. Toro, J. M. Sauder, M. Iizuka, M. Dickey, M. Maletic, S. R. Wasserman, J. Koss, S. K. Burley, S. C. Almo
Crystal Structure Of Mannose-6-Phosphate Isomerase From Helicobacter Pylori.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MANNOSE-6-PHOSPHATE ISOMERASE
    Atcc: 700392
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Taxid: 562
    Expression System Vector: PET
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN
    Gene: HP_0043
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 85962
    Strain: 26695
    Synonym: PMI, ALGA

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2QH5)

(-) Sites  (0, 0)

(no "Site" information available for 2QH5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QH5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2QH5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QH5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QH5)

(-) Exons   (0, 0)

(no "Exon" information available for 2QH5)

(-) 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:253
 aligned with O24884_HELPY | O24884 from UniProtKB/TrEMBL  Length:470

    Alignment length:266
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260      
         O24884_HELPY     1 MKIKNILLSGGSGKRLWPLSRSLYPKQFLKLFDHKSLFELSFKRNASLVDETLIVCNEKHYFLALEEIKNEIKNKSVGFLLESLSKNTANAIALSALMSDKEDLLIVTPSDHLIKDLQAYENAIKKAIDLAQKGFLVTFGVSIDKPNTEFGYIESPNGLDVKRFIEKPSLDKAIEFQKSGGFYFNSGMFVFQAGVFLDELKKHAPTILKGCERAFESLENAYFFEKKIARLSEKSMQDLEDMSIDIALMQQSHKIKMVELNAKWSD 266
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qh5A00 A:             1-266 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..-------------.hhhhh......hhhhhhhhhhhh...eeeeeee..hhhhhhhhh.......eeeeeee...hhhhhhhhhhhhh.....eeeeee......hhhhhhhhhhhhhhhhhh..eeeeeee........eeee........eeee..hhhhhhhhhhhh.eeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhheee......eeeehhhhhhh....hhhhhh......eeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qh5 A   1 LKIKNILLSG-------------YPKQFLKLFDHKSLFELSFKRNASLVDETLIVCNEKHYFLALEEIKNEIKNKSVGFLLESLSKNTANAIALSALMSDKEDLLIVTPSDHLIKDLQAYENAIKKAIDLAQKGFLVTFGVSIDKPNTEFGYIESPNGLDVKRFIEKPSLDKAIEFQKSGGFYFNSGMFVFQAGVFLDELKKHAPTILKGCERAFESLENAYFFEKKIARLSEKSMQDLEDMSIDIALMQQSHKIKMVELNAKWSD 266
                                    10         -   |    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260      
                                    10            24                                                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:256
 aligned with O24884_HELPY | O24884 from UniProtKB/TrEMBL  Length:470

    Alignment length:266
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260      
         O24884_HELPY     1 MKIKNILLSGGSGKRLWPLSRSLYPKQFLKLFDHKSLFELSFKRNASLVDETLIVCNEKHYFLALEEIKNEIKNKSVGFLLESLSKNTANAIALSALMSDKEDLLIVTPSDHLIKDLQAYENAIKKAIDLAQKGFLVTFGVSIDKPNTEFGYIESPNGLDVKRFIEKPSLDKAIEFQKSGGFYFNSGMFVFQAGVFLDELKKHAPTILKGCERAFESLENAYFFEKKIARLSEKSMQDLEDMSIDIALMQQSHKIKMVELNAKWSD 266
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qh5B00 B          :1-266 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                                     CATH domains
           Pfam domains (1) ---NTP_tr          ansferase-2qh5B01 B:4-266                                                                                                                                                                                                                               Pfam domains (1)
           Pfam domains (2) ---NTP_tr          ansferase-2qh5B02 B:4-266                                                                                                                                                                                                                               Pfam domains (2)
         Sec.struct. author ..eeeeee.----------.....hhhhh......hhhhhhhhhhhh...eeeeeee..hhhhhhhhh.......eeeeeee....hhhhhhhhhhhh.....eeeeee......hhhhhhhhhhhhhhhhh...eeeeee..........eee........eee...hhhhhhhhhhhh.eeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh.eeee....eeeeehhhhhh.....hhhhhh......eeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qh5 B   1 LKIKNILLS----------SRSLYPKQFLKLFDHKSLFELSFKRNASLVDETLIVCNEKHYFLALEEIKNEIKNKSVGFLLESLSKNTANAIALSALMSDKEDLLIVTPSDHLIKDLQAYENAIKKAIDLAQKGFLVTFGVSIDKPNTEFGYIESPNGLDVKRFIEKPSLDKAIEFQKSGGFYFNSGMFVFQAGVFLDELKKHAPTILKGCERAFESLENAYFFEKKIARLSEKSMQDLEDMSIDIALMQQSHKIKMVELNAKWSD 266
                                    |-        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260      
                                    9         20
   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 2QH5)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: GT-A (172)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (O24884_HELPY | O24884)
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:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
biological process
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    GO:0000271    polysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
    GO:0005976    polysaccharide metabolic process    The chemical reactions and pathways involving a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.

 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
(no "Ligands, Modified Residues, Ions" information available for 2qh5)
 
  Sites
(no "Sites" information available for 2qh5)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2qh5)
 
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 | Biol. Unit 1 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
  2qh5
    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
  O24884_HELPY | O24884
    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
  O24884_HELPY | O24884
    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 2QH5)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2QH5)