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 :  CRYSTAL STRUCTURE OF A PUTATIVE LIPASE (NP_343859.1) FROM SULFOLOBUS SOLFATARICUS AT 1.85 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  17 Sep 07  (Deposition) - 09 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Np_343859. 1, Putative Lipase, 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 A Putative Lipase (Np_343859. 1) From Sulfolobus Solfataricus At 1. 85 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE ESTERASE
    Atcc: 35092
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NP_343859.1, SSO2518
    Organism Scientific: SULFOLOBUS SOLFATARICUS P2
    Organism Taxid: 273057
    Strain: P2, DSM 1617, JCM 11322

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 15)

Asymmetric Unit (6, 15)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3MSE5Mod. Amino AcidSELENOMETHIONINE
4PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
5PG41Ligand/IonTETRAETHYLENE GLYCOL
6UNL1Ligand/IonUNKNOWN LIGAND
Biological Unit 1 (5, 12)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3MSE5Mod. Amino AcidSELENOMETHIONINE
4PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
5PG41Ligand/IonTETRAETHYLENE GLYCOL
6UNL1Ligand/IonUNKNOWN LIGAND
Biological Unit 2 (5, 24)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3MSE10Mod. Amino AcidSELENOMETHIONINE
4PEG8Ligand/IonDI(HYDROXYETHYL)ETHER
5PG42Ligand/IonTETRAETHYLENE GLYCOL
6UNL2Ligand/IonUNKNOWN LIGAND

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:216 , ILE A:217 , PG4 A:358 , HOH A:393 , HOH A:430BINDING SITE FOR RESIDUE CA A 354
02AC2SOFTWAREGLY A:141 , GLU A:143 , ASP A:239 , EDO A:357 , HOH A:445 , HOH A:486BINDING SITE FOR RESIDUE CA A 355
03AC3SOFTWAREASN A:224 , PRO A:225 , ASP A:226 , HOH A:429 , HOH A:587BINDING SITE FOR RESIDUE CA A 356
04AC4SOFTWAREGLY A:141 , GLN A:142 , GLU A:143 , ASP A:239 , CA A:355 , HOH A:408 , HOH A:445 , HOH A:447 , HOH A:460BINDING SITE FOR RESIDUE EDO A 357
05AC5SOFTWAREARG A:210 , ASN A:215 , ILE A:217 , PRO A:230 , PHE A:240 , SER A:244 , CA A:354 , HOH A:440BINDING SITE FOR RESIDUE PG4 A 358
06AC6SOFTWARETHR A:58 , GLN A:64 , ILE A:68 , LYS A:82 , PHE A:188 , LEU A:245 , ILE A:267 , PHE A:271 , TYR A:332 , HOH A:394 , HOH A:505BINDING SITE FOR RESIDUE UNL A 359
07AC7SOFTWARESER A:151 , PHE A:188 , TYR A:189 , PHE A:309BINDING SITE FOR RESIDUE PEG A 360
08AC8SOFTWAREARG A:138 , ASP A:139 , LYS A:233 , HOH A:671BINDING SITE FOR RESIDUE PEG A 361
09AC9SOFTWARESER A:123 , LYS A:286 , PHE A:287 , HOH A:441BINDING SITE FOR RESIDUE PEG A 362
10BC1SOFTWAREASN A:49 , ASP A:50 , ASN A:91 , GLY A:92BINDING SITE FOR RESIDUE PEG A 363

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:30 -Asp A:31
2Tyr A:256 -Pro A:257

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2RAU)

(-) 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:350
 aligned with Q97VU1_SULSO | Q97VU1 from UniProtKB/TrEMBL  Length:353

    Alignment length:352
                                    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       271       281       291       301       311       321       331       341       351  
         Q97VU1_SULSO     2 YEEWKIVKREAPILGNDQLIENIWKMKREDSPYDIISLHKVNLIGGGNDAVLILPGTWSSGEQLVTISWNGVHYTIPDYRKSIVLYLARNGFNVYTIDYRTHYVPPFLKDRQLSFTANWGWSTWISDIKEVVSFIKRDSGQERIYLAGESFGGIAALNYSSLYWKNDIKGLILLDGGPTKHGIRPKFYTPEVNSIEEMEAKGIYVIPSRGGPNNPIWSYALANPDMPSPDPKYKSISDFLMDSLYVTGSANPYDYPYSKKEDMFPILASFDPYWPYRLSLERDLKFDYEGILVPTIAFVSERFGIQIFDSKILPSNSEIILLKGYGHLDVYTGENSEKDVNSVVLKWLSQQR 353
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2rauA00 A:2-353  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee..eeeeeeeeeeee.......eeeeeeeee....eeeeeee.....hhhhhhhhee..ee....hhhhhhhhhhhhh.eeeeeeehhhhhh....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhheeeeeee..........--.......hhhhhhhhh..eee.......hhhhhhhhh...........hhhhhhhhhhhhh...........hhhhhhhhhhh...eeehhhhhh.............eeeeee..hhhhhhhhhhh....eeeee...hhhhhh...hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rau A   2 YEEWKIVKREAPILGNDQLIENIWKmKREDSPYDIISLHKVNLIGGGNDAVLILPGTWSSGEQLVTISWNGVHYTIPDYRKSIVLYLARNGFNVYTIDYRTHYVPPFLKDRQLSFTANWGWSTWISDIKEVVSFIKRDSGQERIYLAGESFGGIAALNYSSLYWKNDIKGLILLDGGPTKHGIR--FYTPEVNSIEEmEAKGIYVIPSRGGPNNPIWSYALANPDmPSPDPKYKSISDFLmDSLYVTGSANPYDYPYSKKEDmFPILASFDPYWPYRLSLERDLKFDYEGILVPTIAFVSERFGIQIFDSKILPSNSEIILLKGYGHLDVYTGENSEKDVNSVVLKWLSQQR 353
                                    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  |    271       281       291       301       311       321       331       341       351  
                                                    27-MSE                                                                                                                                                       185  |        199-MSE                     227-MSE        242-MSE               264-MSE                                                                                     
                                                                                                                                                                                                                    188
   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 2RAU)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2RAU)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q97VU1_SULSO | Q97VU1)
molecular function
    GO:0016298    lipase activity    Catalysis of the hydrolysis of a lipid or phospholipid.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

 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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PG4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    UNL  [ 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
    Glu A:30 - Asp A:31   [ RasMol ]  
    Tyr A:256 - Pro A:257   [ 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
  2rau
    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
  Q97VU1_SULSO | Q97VU1
    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
  Q97VU1_SULSO | Q97VU1
    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 2RAU)

(-) Related Entries Specified in the PDB File

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