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

(-) Description

Title :  CRYSTAL STRUCTURE OF A GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE (BDI_3922) FROM PARABACTEROIDES DISTASONIS ATCC 8503 AT 1.55 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  11 May 10  (Deposition) - 07 Jul 10  (Release) - 07 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A,B
Keywords :  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 Glycerophosphoryl Diester Phosphodiesterase (Bdi_3922) From Parabacteroides Distasoni Atcc 8503 At 1. 55 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BDI_3922
    Organism Scientific: PARABACTEROIDES DISTASONIS
    Organism Taxid: 435591
    Strain: ATCC 8503 / DSM 20701 / NCTC 11152

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 45)

Asymmetric/Biological Unit (5, 45)
No.NameCountTypeFull Name
1MSE22Mod. Amino AcidSELENOMETHIONINE
2NA1Ligand/IonSODIUM ION
3PE41Ligand/Ion2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
4PG49Ligand/IonTETRAETHYLENE GLYCOL
5SO412Ligand/IonSULFATE ION

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:61 , ARG A:62 , HIS A:104 , HOH A:347 , HOH A:356 , HOH A:501BINDING SITE FOR RESIDUE SO4 A 2
02AC2SOFTWAREMSE A:247 , GLU A:250 , ARG A:251BINDING SITE FOR RESIDUE SO4 A 5
03AC3SOFTWARELYS A:163 , PRO A:167 , MSE A:168 , HOH A:397 , HOH A:425 , HOH A:500 , HOH A:504BINDING SITE FOR RESIDUE SO4 A 7
04AC4SOFTWAREARG A:65 , ASP A:264 , LYS A:265 , ARG A:291 , HOH A:375 , HOH A:438 , HOH A:569BINDING SITE FOR RESIDUE SO4 A 8
05AC5SOFTWAREARG A:62 , ARG A:65 , LYS A:265 , HOH A:319 , HOH A:325 , LYS B:117BINDING SITE FOR RESIDUE SO4 A 9
06AC6SOFTWAREARG A:54 , LEU A:302 , HOH A:510 , HOH A:554BINDING SITE FOR RESIDUE PG4 A 17
07AC7SOFTWARELYS A:236BINDING SITE FOR RESIDUE PG4 A 19
08AC8SOFTWAREPRO A:56 , THR A:84 , ALA A:296 , HOH A:363BINDING SITE FOR RESIDUE PG4 A 21
09AC9SOFTWAREILE A:38 , ARG A:154 , GLN A:179 , TYR A:183 , ARG B:154BINDING SITE FOR RESIDUE PG4 A 23
10BC1SOFTWAREPE4 B:14BINDING SITE FOR RESIDUE NA B 1
11BC2SOFTWAREHIS B:61 , ARG B:62 , HIS B:104 , HOH B:335 , HOH B:351 , HOH B:501 , HOH B:553BINDING SITE FOR RESIDUE SO4 B 3
12BC3SOFTWARELYS A:117 , ARG B:62 , ARG B:65 , LYS B:265 , HOH B:372 , HOH B:375 , HOH B:539 , HOH B:559BINDING SITE FOR RESIDUE SO4 B 4
13BC4SOFTWARELYS B:163 , PRO B:167 , MSE B:168 , HOH B:345BINDING SITE FOR RESIDUE SO4 B 6
14BC5SOFTWAREMSE B:247 , GLU B:250 , ARG B:251BINDING SITE FOR RESIDUE SO4 B 10
15BC6SOFTWAREARG B:65 , ASP B:264 , LYS B:265 , ARG B:291 , HOH B:386 , HOH B:440 , HOH B:536BINDING SITE FOR RESIDUE SO4 B 11
16BC7SOFTWAREGLU B:135 , ARG B:291 , HOH B:471BINDING SITE FOR RESIDUE SO4 B 12
17BC8SOFTWAREARG B:93 , LYS B:164 , HOH B:394BINDING SITE FOR RESIDUE SO4 B 13
18BC9SOFTWARENA B:1 , ASP B:97 , SER B:98 , TRP B:123 , ARG B:170BINDING SITE FOR RESIDUE PE4 B 14
19CC1SOFTWAREPG4 B:16 , LYS B:236BINDING SITE FOR RESIDUE PG4 B 15
20CC2SOFTWAREPG4 B:15 , LYS B:236BINDING SITE FOR RESIDUE PG4 B 16
21CC3SOFTWAREASP A:221 , HOH B:463BINDING SITE FOR RESIDUE PG4 B 18
22CC4SOFTWAREILE B:55 , PRO B:56 , LEU B:57 , THR B:84 , ALA B:296 , SER B:300 , HOH B:420BINDING SITE FOR RESIDUE PG4 B 20
23CC5SOFTWAREPRO A:202 , GLU B:109 , SER B:112 , ASN B:113 , GLY B:114 , LYS B:132BINDING SITE FOR RESIDUE PG4 B 22

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MZ2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MZ2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MZ2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MZ2)

(-) Exons   (0, 0)

(no "Exon" information available for 3MZ2)

(-) Sequences/Alignments

Asymmetric/Biological 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:285
 aligned with A6LIT8_PARD8 | A6LIT8 from UniProtKB/TrEMBL  Length:316

    Alignment length:285
                                    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     
         A6LIT8_PARD8    32 GMNTLQISNVDDLISFYQYADDRIPLISGHRGGRGKGYPENSMETFENTLSYTPATFEIDPRLTKDSVIVLFHDDTLERTSNGTGKVSDYTWEELQNFRLKDPEGNITNYRIPTLEEAIRWARGKTILILDKKDVPMERTAQLITDMQAEPYVMITVHDGASARFFYEKNPNFMFEAFVKTKEAVQDYEDNGIPWSHIMAYVGPKITPEVREVIDMLHERGVMCMISTAPSDDKLSTPESRAEAYRMIIRQGVDIIESDRPIEVAEAISSLIPVSSSKGKFFSTL 316
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...hhhhhhhhh........eeee.hhh........hhhhhhhhhhhh..eeee.eee.....eee..............hhhhhhhhhhh.................hhhhhhhhhh....eee.....hhhhhhhhhhhh.....eeeee.hhhhhhhhhhhh....eeee..hhhhhhhhhhh..hhh.eeeeee...hhhhhhhhhhhhhh...eeee...hhhhh.hhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhh.....hhh.eeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mz2 A  32 GmNTLQISNVDDLISFYQYADDRIPLISGHRGGRGKGYPENSmETFENTLSYTPATFEIDPRLTKDSVIVLFHDDTLERTSNGTGKVSDYTWEELQNFRLKDPEGNITNYRIPTLEEAIRWARGKTILILDKKDVPmERTAQLITDmQAEPYVmITVHDGASARFFYEKNPNFmFEAFVKTKEAVQDYEDNGIPWSHImAYVGPKITPEVREVIDmLHERGVmCmISTAPSDDKLSTPESRAEAYRmIIRQGVDIIESDRPIEVAEAISSLIPVSSSKGKFFSTL 316
                             |      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     
                             |                                       74-MSE                                                                                       168-MSE   178-MSE  |                 205-MSE                  230-MSE          247-MSE  | |                   278-MSE                                  
                            33-MSE                                                                                                                                                 185-MSE                                                              254-MSE                                                          
                                                                                                                                                                                                                                                          256-MSE                                                        


Chain B from PDB  Type:PROTEIN  Length:285
 aligned with A6LIT8_PARD8 | A6LIT8 from UniProtKB/TrEMBL  Length:316

    Alignment length:285
                                    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     
         A6LIT8_PARD8    32 GMNTLQISNVDDLISFYQYADDRIPLISGHRGGRGKGYPENSMETFENTLSYTPATFEIDPRLTKDSVIVLFHDDTLERTSNGTGKVSDYTWEELQNFRLKDPEGNITNYRIPTLEEAIRWARGKTILILDKKDVPMERTAQLITDMQAEPYVMITVHDGASARFFYEKNPNFMFEAFVKTKEAVQDYEDNGIPWSHIMAYVGPKITPEVREVIDMLHERGVMCMISTAPSDDKLSTPESRAEAYRMIIRQGVDIIESDRPIEVAEAISSLIPVSSSKGKFFSTL 316
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------GDPD-3mz2B01 B:61-260                                                                                                                                                                                   -------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------GDPD-3mz2B02 B:61-260                                                                                                                                                                                   -------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .eeee...hhhhhhhhh........eeee.hhh........hhhhhhhhhhhh..eeee.eee.....eee..............hhhhhhhhhhh.................hhhhhhhhhh....eee.....hhhhhhhhhhhh.....eeeee.hhhhhhhhhhhh....eeee..hhhhhhhhhhh..hhh.eeeeee...hhhhhhhhhhhhhh...eeee...hhhhh.hhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhh.....hhh.eeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mz2 B  32 GmNTLQISNVDDLISFYQYADDRIPLISGHRGGRGKGYPENSmETFENTLSYTPATFEIDPRLTKDSVIVLFHDDTLERTSNGTGKVSDYTWEELQNFRLKDPEGNITNYRIPTLEEAIRWARGKTILILDKKDVPmERTAQLITDmQAEPYVmITVHDGASARFFYEKNPNFmFEAFVKTKEAVQDYEDNGIPWSHImAYVGPKITPEVREVIDmLHERGVmCmISTAPSDDKLSTPESRAEAYRmIIRQGVDIIESDRPIEVAEAISSLIPVSSSKGKFFSTL 316
                             |      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     
                            33-MSE                                   74-MSE                                                                                       168-MSE   178-MSE  |                 205-MSE                  230-MSE          247-MSE  | |                   278-MSE                                  
                                                                                                                                                                                   185-MSE                                                              254-MSE                                                          
                                                                                                                                                                                                                                                          256-MSE
   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 3MZ2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MZ2)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: PLC (20)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (A6LIT8_PARD8 | A6LIT8)
molecular function
    GO:0008889    glycerophosphodiester phosphodiesterase activity    Catalysis of the reaction: a glycerophosphodiester + H2O = an alcohol + sn-glycerol 3-phosphate.
    GO:0008081    phosphoric diester hydrolase activity    Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
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.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PE4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PG4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
    CC3  [ RasMol ]  +environment [ RasMol ]
    CC4  [ RasMol ]  +environment [ RasMol ]
    CC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3mz2)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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
  3mz2
    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
  A6LIT8_PARD8 | A6LIT8
    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
  A6LIT8_PARD8 | A6LIT8
    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 3MZ2)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3MZ2)