Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
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 EST25 - A BACTERIAL HOMOLOG OF HORMONE-SENSITIVE LIPASE FROM A METAGENOMIC LIBRARY
 
Authors :  T. D. Ngo, B. H. Ryu, H. S. Ju, E. J. Jang, K. S. Park, S. B. Joo, K. K. Kim, D. H
Date :  13 Feb 13  (Deposition) - 15 Jan 14  (Release) - 15 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.49
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Alpha/Beta, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. D. Ngo, B. H. Ryu, H. Ju, E. Jang, K. Park, K. K. Kim, D. H. Kim
Structural And Functional Analyses Of A Bacterial Homologue Of Hormone-Sensitive Lipase From A Metagenomic Library
Acta Crystallogr. , Sect. D V. 69 1726 2014
PubMed-ID: 23999296  |  Reference-DOI: 10.1107/S0907444913013425

(-) Compounds

Molecule 1 - ESTERASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Strain: XL1-BLUE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: UNCULTURED BACTERIUM
    Organism Taxid: 77133

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4J7A)

(-) Sites  (0, 0)

(no "Site" information available for 4J7A)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4J7A)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Gly A:165 -Asn A:166
2Phe A:169 -Pro A:170
3Gly B:165 -Asn B:166
4Phe B:169 -Pro B:170
5Gly C:165 -Asn C:166
6Phe C:169 -Pro C:170
7Gly D:165 -Asn D:166
8Phe D:169 -Pro D:170

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J7A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J7A)

(-) Exons   (0, 0)

(no "Exon" information available for 4J7A)

(-) 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:355
                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4j7aa_ A: automated matches                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh...........hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeeee.....eeeeeeeee.........eeeeeee...........hhhhhhhhhhhhhh..eeeeee....hhhhh....hhhhhhhhhhhhhhhhhhhhhheeeeeeeeehhhhhhhhhhhhhhhhh.hhhhh.eeeee...............hhhhhh.....hhhhhhhhhhhhh...........hhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhh...eeeeee.....hhhhh....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j7a A   8 QLPGRLGDPSMSLGTDPRTDPRLAAALTQLGLADQAAEPPVNANSEVADCIAYSTAAEQAWQTLFAMLGSQGEPSNPVDVREETIKGRGGNEIKLYIHSPTGHTSDSDPLPCVVHTHGGGMVILTAADANYSRWRSELAATGLVVVGVEFRNAAGALGNHPFPAGLHDCADAAKWVASNREALGISTLIMSGESGGGNLSLATTMLAKKEGWLEEIAGVYAQCPYISGLYASKPEELPSLLENDAYFLDMKTMGAMVKPYDPTGENASNPLAWPYHASLEDLAGLPPHVISVNELDPLRDEGLAHYRKLLKAGVSTVGRTVHGTCHAADCSFVDVIPDVYFATVRDISAFAYSRA 362
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357     


Chain B from PDB  Type:PROTEIN  Length:355
                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4j7ab_ B: automated matches                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh...........hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeeee.....eeeeeeeee.........eeeeee............hhhhhhhhhhhhhh..eeeeee....hhhhh....hhhhhhhhhhhhhhhhhhhhhheeeeeeeeehhhhhhhhhhhhhhhhhhhhhhh.eeeee...............hhhhhh.....hhhhhhhhhhhhh...........hhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhh...eeeeee.....hhhhh....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j7a B   8 QLPGRLGDPSMSLGTDPRTDPRLAAALTQLGLADQAAEPPVNANSEVADCIAYSTAAEQAWQTLFAMLGSQGEPSNPVDVREETIKGRGGNEIKLYIHSPTGHTSDSDPLPCVVHTHGGGMVILTAADANYSRWRSELAATGLVVVGVEFRNAAGALGNHPFPAGLHDCADAAKWVASNREALGISTLIMSGESGGGNLSLATTMLAKKEGWLEEIAGVYAQCPYISGLYASKPEELPSLLENDAYFLDMKTMGAMVKPYDPTGENASNPLAWPYHASLEDLAGLPPHVISVNELDPLRDEGLAHYRKLLKAGVSTVGRTVHGTCHAADCSFVDVIPDVYFATVRDISAFAYSRA 362
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357     


Chain C from PDB  Type:PROTEIN  Length:355
                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4j7ac_ C: automated matches                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh...........hhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeeee.....eeeeeeeee.........eeeeee............hhhhhhhhhhhhhh..eeeeee....hhhhh....hhhhhhhhhhhhhhhhhhhhhheeeeeeeeehhhhhhhhhhhhhhhhhhhhhhh.eeeee...............hhhhhh.....hhhhhhhhhhhhh...........hhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhh...eeeeee.....hhhhh....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j7a C   8 QLPGRLGDPSMSLGTDPRTDPRLAAALTQLGLADQAAEPPVNANSEVADCIAYSTAAEQAWQTLFAMLGSQGEPSNPVDVREETIKGRGGNEIKLYIHSPTGHTSDSDPLPCVVHTHGGGMVILTAADANYSRWRSELAATGLVVVGVEFRNAAGALGNHPFPAGLHDCADAAKWVASNREALGISTLIMSGESGGGNLSLATTMLAKKEGWLEEIAGVYAQCPYISGLYASKPEELPSLLENDAYFLDMKTMGAMVKPYDPTGENASNPLAWPYHASLEDLAGLPPHVISVNELDPLRDEGLAHYRKLLKAGVSTVGRTVHGTCHAADCSFVDVIPDVYFATVRDISAFAYSRA 362
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357     


Chain D from PDB  Type:PROTEIN  Length:355
                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4j7ad_ D: automated matches                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh...........hhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeeee.....eeeeeeeee.........eeeeee............hhhhhhhhhhhhhh..eeeeee....hhhhh....hhhhhhhhhhhhhhhhhhhhhheeeeeeeeehhhhhhhhhhhhhhhhhhhhhhh.eeeee...............hhhhhh.....hhhhhhhhhhhhh...........hhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhh...eeeeee.....hhhhh....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j7a D   8 QLPGRLGDPSMSLGTDPRTDPRLAAALTQLGLADQAAEPPVNANSEVADCIAYSTAAEQAWQTLFAMLGSQGEPSNPVDVREETIKGRGGNEIKLYIHSPTGHTSDSDPLPCVVHTHGGGMVILTAADANYSRWRSELAATGLVVVGVEFRNAAGALGNHPFPAGLHDCADAAKWVASNREALGISTLIMSGESGGGNLSLATTMLAKKEGWLEEIAGVYAQCPYISGLYASKPEELPSLLENDAYFLDMKTMGAMVKPYDPTGENASNPLAWPYHASLEDLAGLPPHVISVNELDPLRDEGLAHYRKLLKAGVSTVGRTVHGTCHAADCSFVDVIPDVYFATVRDISAFAYSRA 362
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J7A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J7A)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

 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 4j7a)
 
  Sites
(no "Sites" information available for 4j7a)
 
  Cis Peptide Bonds
    Gly A:165 - Asn A:166   [ RasMol ]  
    Gly B:165 - Asn B:166   [ RasMol ]  
    Gly C:165 - Asn C:166   [ RasMol ]  
    Gly D:165 - Asn D:166   [ RasMol ]  
    Phe A:169 - Pro A:170   [ RasMol ]  
    Phe B:169 - Pro B:170   [ RasMol ]  
    Phe C:169 - Pro C:170   [ RasMol ]  
    Phe D:169 - Pro D:170   [ 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 | 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
  4j7a
    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
  Q4TZQ3_9BACT | Q4TZQ3
    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
  Q4TZQ3_9BACT | Q4TZQ3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q4TZQ3_9BACT | Q4TZQ3: 5iq0 5iq2 5iq3

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4J7A)