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 :  AQUIFEX AEOLICUS KDO8P SYNTHASE IN COMPLEX WITH CADMIUM
 
Authors :  H. S. Duewel, S. Radaev, J. Wang, R. W. Woodard, D. L. Gatti
Date :  26 Sep 00  (Deposition) - 21 Apr 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Kdo8Ps, Kdo8P, Kdo, Pep, A5P, Beta/Alpha Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. S. Duewel, S. Radaev, J. Wang, R. W. Woodard, D. L. Gatti
Substrate And Metal Complexes Of 3-Deoxy-D-Manno-Octulosonate-8-Phosphate Synthase From Aquifex Aeolicus At 1. 9-A Resolution. Implications For The Condensation Mechanism.
J. Biol. Chem. V. 276 8393 2001
PubMed-ID: 11115499  |  Reference-DOI: 10.1074/JBC.M007884200

(-) Compounds

Molecule 1 - 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE
    Chains: A, B
    EC Number: 4.1.2.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PAAKDSA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363
    Synonym: KDO8P SYNTHASE, PHOSPHO-2-DEHYDRO-3-DEOXYOCTONATE ALDOLASE, 3-DEOXY-D-MANNO-OCTULOSONIC ACID 8-PHOSPHATE SYNTHETASE, KDO-8- PHOSPHATE SYNTHETASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1CD2Ligand/IonCADMIUM ION
2PO44Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2PO48Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:1101 , ALA A:1102 , LYS A:1124 , ARG A:1154 , HOH A:3016 , HOH A:3047 , HOH A:3069BINDING SITE FOR RESIDUE PO4 A 1268
2AC2SOFTWAREPRO B:2101 , ALA B:2102 , LYS B:2124 , ARG B:2154 , HOH B:3014 , HOH B:3029 , HOH B:3060BINDING SITE FOR RESIDUE PO4 B 2268
3AC3SOFTWAREARG A:1049 , SER A:1050 , HOH A:3028BINDING SITE FOR RESIDUE PO4 A 1269
4AC4SOFTWAREARG A:1106 , ARG B:2049 , SER B:2050 , HOH B:3058BINDING SITE FOR RESIDUE PO4 B 2269
5AC5SOFTWARECYS A:1011 , HIS A:1185 , GLU A:1222 , ASP A:1233 , HOH A:3179BINDING SITE FOR RESIDUE CD A 1270
6AC6SOFTWARECYS B:2011 , HIS B:2185 , GLU B:2222 , ASP B:2233BINDING SITE FOR RESIDUE CD B 2270

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1FXP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1FXP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1FXP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1FXP)

(-) Exons   (0, 0)

(no "Exon" information available for 1FXP)

(-) 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 KDSA_AQUAE | O66496 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:263
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261   
          KDSA_AQUAE      2 EKFLVIAGPCAIESEELLLKVGEEIKRLSEKFKEVEFVFKSSFDKANRSSIHSFRGHGLEYGVKALRKVKEEFGLKITTDIHESWQAEPVAEVADIIQIPAFLCRQTDLLLAAAKTGRAVNVKKGQFLAPWDTKNVVEKLKFGGAKEIYLTERGTTFGYNNLVVDFRSLPIMKQWAKVIYDATHSVQLPGGLGDKSGGMREFIFPLIRAAVAVGCDGVFMETHPEPEKALSDASTQLPLSQLEGIIEAILEIREVASKYYETI  264
               SCOP domains d1fxpa_ A: 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8P synthase)                                                                                                                                                                                           SCOP domains
               CATH domains 1fxpA00 A:1002-1264 Aldolase class I                                                                                                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhh.........................hhhhhhhhhhhhhhhhh........hhhhhhhhhh.......hhhhh.hhhhhhhhhh.............hhhhhhhhhhhhhhh...........ee.....ee...hhhhhhh................----------..hhhhhhhhhhhhh..........hhhhh...........hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1fxp A 1002 EKFLVIAGPCAIESEELLLKVGEEIKRLSEKFKEVEFVFKSSFDKANRSSIHSFRGHGLEYGVKALRKVKEEFGLKITTDIHESWQAEPVAEVADIIQIPAFLCRQTDLLLAAAKTGRAVNVKKGQFLAPWDTKNVVEKLKFGGAKEIYLTERGTTFGYNNLVVDFRSLPIMKQWAKVIYDATHSVQLP----------REFIFPLIRAAVAVGCDGVFMETHPEPEKALSDASTQLPLSQLEGIIEAILEIREVASKYYETI 1264
                                  1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161      1171      1181        |-      1201      1211      1221      1231      1241      1251      1261   
                                                                                                                                                                                                                     1190       1201                                                               


Chain B from PDB  Type:PROTEIN  Length:250
 aligned with KDSA_AQUAE | O66496 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:262
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262  
          KDSA_AQUAE      3 KFLVIAGPCAIESEELLLKVGEEIKRLSEKFKEVEFVFKSSFDKANRSSIHSFRGHGLEYGVKALRKVKEEFGLKITTDIHESWQAEPVAEVADIIQIPAFLCRQTDLLLAAAKTGRAVNVKKGQFLAPWDTKNVVEKLKFGGAKEIYLTERGTTFGYNNLVVDFRSLPIMKQWAKVIYDATHSVQLPGGLGDKSGGMREFIFPLIRAAVAVGCDGVFMETHPEPEKALSDASTQLPLSQLEGIIEAILEIREVASKYYETI  264
               SCOP domains d1fxpb_ B: 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8P synthase)                                                                                                                                                                                          SCOP domains
               CATH domains 1fxpB00 B:2003-2264 Aldolase class I                                                                                                                                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhhhhh.........................hhhhhhhhhhhhhhhhh........hhhhhhhhh........hhhhh.hhhhhhhhhhh............hhhhhhhhhhhhhhh...........ee.....ee...hhhhhhh..............------------..hhhhhhhhhhhhh..........hhhhh...........hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1fxp B 2003 KFLVIAGPCAIESEELLLKVGEEIKRLSEKFKEVEFVFKSSFDKANRSSIHSFRGHGLEYGVKALRKVKEEFGLKITTDIHESWQAEPVAEVADIIQIPAFLCRQTDLLLAAAKTGRAVNVKKGQFLAPWDTKNVVEKLKFGGAKEIYLTERGTTFGYNNLVVDFRSLPIMKQWAKVIYDATHSVQ------------REFIFPLIRAAVAVGCDGVFMETHPEPEKALSDASTQLPLSQLEGIIEAILEIREVASKYYETI 2264
                                  2012      2022      2032      2042      2052      2062      2072      2082      2092      2102      2112      2122      2132      2142      2152      2162      2172      2182     |   -      2202      2212      2222      2232      2242      2252      2262  
                                                                                                                                                                                                                  2188         2201
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1FXP)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (KDSA_AQUAE | O66496)
molecular function
    GO:0008676    3-deoxy-8-phosphooctulonate synthase activity    Catalysis of the reaction: D-arabinose 5-phosphate + H(2)O + phosphoenolpyruvate = 8-phospho-3-deoxy-D-manno-oct-2-ulosonate + 2 H(+) + phosphate.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
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:0019294    keto-3-deoxy-D-manno-octulosonic acid biosynthetic process    The chemical reactions and pathways resulting in the formation of keto-3-deoxy-D-manno-octulosonic acid, an acidic sugar present in lipopolysaccharides of the outer membranes of some Gram-negative bacteria.
    GO:0009103    lipopolysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 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
    CD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1fxp)
 
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
  1fxp
    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
  KDSA_AQUAE | O66496
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  4.1.2.16
    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
  KDSA_AQUAE | O66496
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        KDSA_AQUAE | O66496: 1fwn 1fws 1fwt 1fww 1fx6 1fxq 1fy6 1jcx 1jcy 1lrn 1lro 1lrq 1pck 1pcw 1pe1 1t8x 1t96 1t99 1zha 1zji 2a21 2a2i 2ef9 2nwr 2nws 2nx1 2nx3 2nxg 2nxh 2nxi 3e0i 3e12

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1FXP)