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
(-)Biological Unit 2
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  A. FULGIDUS LIPASE WITH FATTY ACID FRAGMENT AND MAGNESIUM
 
Authors :  C. K. Chen, T. P. Ko, R. T. Guo, A. H. Wang
Date :  28 Jan 09  (Deposition) - 16 Jun 09  (Release) - 05 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.77
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Lipase, Archaeoglobus Fulgidus, Fatty Acid, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. K. Chen, G. C. Lee, T. P. Ko, R. T. Guo, L. M. Huang, H. J. Liu, Y. F. Ho, J. F. Shaw, A. H. Wang
Structure Of The Alkalohyperthermophilic Archaeoglobus Fulgidus Lipase Contains A Unique C-Terminal Domain Essential For Long-Chain Substrate Binding.
J. Mol. Biol. V. 390 672 2009
PubMed-ID: 19447113  |  Reference-DOI: 10.1016/J.JMB.2009.05.017

(-) Compounds

Molecule 1 - LIPASE, PUTATIVE
    Chains: A, B
    EC Number: 3.1.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-23A(+)
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AF_1763
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 2234

 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  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
11PE2Ligand/IonPENTAETHYLENE GLYCOL
2MG5Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:31 , HIS A:135 , PHE A:254 , LEU A:330 , SER A:332 , GLU A:339 , PHE A:426BINDING SITE FOR RESIDUE 1PE A 500
2AC2SOFTWAREHIS A:158 , HOH A:679 , HOH A:680 , HOH A:681 , HOH A:682 , HOH A:732BINDING SITE FOR RESIDUE MG A2001
3AC3SOFTWAREHOH A:870 , HOH A:872 , HOH A:873 , HOH A:874 , HOH A:1138BINDING SITE FOR RESIDUE MG A2002
4AC4SOFTWAREASP A:405 , ARG A:406 , ASP A:409 , LYS A:411 , ASP A:431 , HOH A:845BINDING SITE FOR RESIDUE MG A2003
5AC5SOFTWARELEU B:31 , ALA B:32 , VAL B:338 , PHE B:426 , HOH B:871BINDING SITE FOR RESIDUE 1PE B 500
6AC6SOFTWAREASP B:405 , ARG B:406 , ASP B:409 , LYS B:411 , ASP B:431 , HOH B:804BINDING SITE FOR RESIDUE MG B2004
7AC7SOFTWAREHIS B:158 , HOH B:726 , HOH B:727 , HOH B:867 , HOH B:1235 , HOH B:1236BINDING SITE FOR RESIDUE MG B2005

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:334 -Pro A:335
2Pro B:334 -Pro B:335

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2ZYR)

(-) 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:464
 aligned with O28511_ARCFU | O28511 from UniProtKB/TrEMBL  Length:474

    Alignment length:464
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               474          
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470   |     -    
         O28511_ARCFU    21 DFRPVVFVHGLAGSAGQFESQGMRFAANGYPAEYVKTFEYDTISWALVVETDMLFSGLGSEFGLNISQIIDPETLDKILSKSRERLIDETFSRLDRVIDEALAESGADKVDLVGHSMGTFFLVRYVNSSPERAAKVAHLILLDGVWGVDAPEGIPTLAVFGNPKALPALGLPEEKVVYNATNVYFNNMTHVQLCTSPETFAVMFEFINGYKPATTDIVPQDGDYVKVKGKFLAFATNGDVSGWLSIYPIDENGKRLTRLPVKFMRVKGDFEVRLRKGQLYEFQFRKDFSPIIYHYYRAPFVRDDLWARFLVSKPPLDVELLILPERLSPAAKETSGLLLIRYKEMIGEYDEEIGGVDEVYVNGVNVCTERICPIERAVNGLWVFDRGADGKSDLDREVVRYSIMPFMSAADLVVPAEGTISIAVKSRTGGEESFTIPAWSADRHSIIVQFSDYI----------   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.....hhhhhhhhhhhhhhh..hhh.eeee..hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhhhheeeeeee.............eeeeee.hhhh..............eeeee...hhhhhhhhhhhhhhhhhhhhh..............eeeeeeeeee.......eeeeeeee.............eeeeee.eeeeeee....eeeeeee.....eeeeee......eeeeeeee.....hhhhhhhhhhhhhhhhh...eeeeeeeee............eeee..ee.......hhhhheeeeeeehhhhh........hhhhh....eeeee.......eeeeeee.....eeeeeee......eeeeee......hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zyr A  21 DFRPVVFVHGLAGSAGQFESQGMRFAANGYPAEYVKTFEYDTISWALVVETDMLFSGLGSEFGLNISQIIDPETLDKILSKSRERLIDETFSRLDRVIDEALAESGADKVDLVGHSMGTFFLVRYVNSSPERAAKVAHLILLDGVWGVDAPEGIPTLAVFGNPKALPALGLPEEKVVYNATNVYFNNMTHVQLCTSPETFAVMFEFINGYKPATTDIVPQDGDYVKVKGKFLAFATNGDVSGWLSIYPIDENGKRLTRLPVKFMRVKGDFEVRLRKGQLYEFQFRKDFSPIIYHYYRAPFVRDDLWARFLVSKPPLDVELLILPERLSPAAKETSGLLLIRYKEMIGEYDEEIGGVDEVYVNGVNVCTERICPIERAVNGLWVFDRGADGKSDLDREVVRYSIMPFMSAADLVVPAEGTISIAVKSRTGGEESFTIPAWSADRHSIIVQFSDYIVDKLAAALEH 484
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480    


Chain B from PDB  Type:PROTEIN  Length:454
 aligned with O28511_ARCFU | O28511 from UniProtKB/TrEMBL  Length:474

    Alignment length:454
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470    
         O28511_ARCFU    21 DFRPVVFVHGLAGSAGQFESQGMRFAANGYPAEYVKTFEYDTISWALVVETDMLFSGLGSEFGLNISQIIDPETLDKILSKSRERLIDETFSRLDRVIDEALAESGADKVDLVGHSMGTFFLVRYVNSSPERAAKVAHLILLDGVWGVDAPEGIPTLAVFGNPKALPALGLPEEKVVYNATNVYFNNMTHVQLCTSPETFAVMFEFINGYKPATTDIVPQDGDYVKVKGKFLAFATNGDVSGWLSIYPIDENGKRLTRLPVKFMRVKGDFEVRLRKGQLYEFQFRKDFSPIIYHYYRAPFVRDDLWARFLVSKPPLDVELLILPERLSPAAKETSGLLLIRYKEMIGEYDEEIGGVDEVYVNGVNVCTERICPIERAVNGLWVFDRGADGKSDLDREVVRYSIMPFMSAADLVVPAEGTISIAVKSRTGGEESFTIPAWSADRHSIIVQFSDYI 474
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----Abhydrolase_6-2zyrB01 B:25-237                                                                                                                                                                                       --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----Abhydrolase_6-2zyrB02 B:25-237                                                                                                                                                                                       --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ....eeee.....hhhhhhhhhhhhhhh..hhh.eeee..hhhhhhhhh.........hhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhhhheeeeeee.............eeeee.hhhhhhhhh..........eeee....hhhhhhhhhhhhhhhhhhhhh..............eeeeeeeeee.......eeeeeeee.............eeeeee.eeeeeee....eeeeeee.....eeeeee......eeeeeeee.....hhhhhhhhhhhhhhhhh...eeee.................eeee..ee.......hhhhh..eeeeehhhhh........hhhhh....eeeee.......eeeeeee.....eeeeeee......eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zyr B  21 DFRPVVFVHGLAGSAGQFESQGMRFAANGYPAEYVKTFEYDTISWALVVETDMLFSGLGSEFGLNISQIIDPETLDKILSKSRERLIDETFSRLDRVIDEALAESGADKVDLVGHSMGTFFLVRYVNSSPERAAKVAHLILLDGVWGVDAPEGIPTLAVFGNPKALPALGLPEEKVVYNATNVYFNNMTHVQLCTSPETFAVMFEFINGYKPATTDIVPQDGDYVKVKGKFLAFATNGDVSGWLSIYPIDENGKRLTRLPVKFMRVKGDFEVRLRKGQLYEFQFRKDFSPIIYHYYRAPFVRDDLWARFLVSKPPLDVELLILPERLSPAAKETSGLLLIRYKEMIGEYDEEIGGVDEVYVNGVNVCTERICPIERAVNGLWVFDRGADGKSDLDREVVRYSIMPFMSAADLVVPAEGTISIAVKSRTGGEESFTIPAWSADRHSIIVQFSDYI 474
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470
   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 2ZYR)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ZYR)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: AB_hydrolase (347)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (O28511_ARCFU | O28511)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

 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
    1PE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ 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
    Pro A:334 - Pro A:335   [ RasMol ]  
    Pro B:334 - Pro B:335   [ 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
  2zyr
    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
  O28511_ARCFU | O28511
    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)
  3.1.1.3
    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
  O28511_ARCFU | O28511
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        O28511_ARCFU | O28511: 2zyh 2zyi 2zys

(-) Related Entries Specified in the PDB File

2zyh 2zyi 2zys