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 :  CRYSTAL STRUCTURE OF AMIDOHYDROLASE PMI1525 (TARGET EFI-500319) FROM PROTEUS MIRABILIS HI4320
 
Authors :  Y. Patskovsky, B. Hillerich, R. D. Seidel, W. D. Zencheck, R. Toro, H. J. F. M. Raushel, J. A. Gerlt, S. C. Almo, Enzyme Function Initiative (
Date :  11 Apr 11  (Deposition) - 27 Apr 11  (Release) - 27 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.53
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hydrolase, Amidohydrolase, Zinc Binding Site, Enzyme Function Initiative, Efi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, B. Hillerich, R. D. Seidel, W. D. Zencheck, R. Toro, H. J. Imker, F. M. Raushel, J. A. Gerlt, S. C. Almo
Crystal Structure Of Amidohydrolase Pmi1525 From Proteus Mirabilis Hi4320
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE PHOPHOTRIESTERASE
    Chains: A
    Engineered: YES
    Gene: PMI1525
    Organism Scientific: PROTEUS MIRABILIS
    Organism Taxid: 529507
    Strain: HI4320

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric Unit (5, 8)
No.NameCountTypeFull Name
1BEZ1Ligand/IonBENZOIC ACID
2CAC1Ligand/IonCACODYLATE ION
3SO41Ligand/IonSULFATE ION
4UNL3Ligand/IonUNKNOWN LIGAND
5ZN2Ligand/IonZINC ION
Biological Unit 1 (4, 12)
No.NameCountTypeFull Name
1BEZ2Ligand/IonBENZOIC ACID
2CAC2Ligand/IonCACODYLATE ION
3SO42Ligand/IonSULFATE ION
4UNL6Ligand/IonUNKNOWN LIGAND
5ZN-1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:23 , HIS A:25 , GLU A:166 , ASP A:294 , CAC A:370BINDING SITE FOR RESIDUE ZN A 367
2AC2SOFTWAREGLU A:166 , HIS A:199 , HIS A:229 , CAC A:370BINDING SITE FOR RESIDUE ZN A 368
3AC3SOFTWAREHIS A:199 , HIS A:229 , PHE A:261 , ASP A:294 , CAC A:370 , HOH A:432 , HOH A:633 , HOH A:649 , HOH A:654BINDING SITE FOR RESIDUE BEZ A 369
4AC4SOFTWAREHIS A:23 , HIS A:25 , TYR A:126 , GLU A:166 , HIS A:199 , HIS A:229 , ASP A:294 , PHE A:296 , ZN A:367 , ZN A:368 , BEZ A:369BINDING SITE FOR RESIDUE CAC A 370
5AC5SOFTWAREMET A:1 , LYS A:2 , GLY A:3 , LYS A:14 , ALA A:344 , GLU A:345 , HOH A:388 , HOH A:406 , HOH A:588 , HOH A:719BINDING SITE FOR RESIDUE SO4 A 371

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:165 -Glu A:166

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3RHG)

(-) 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:363
 aligned with B4EXV8_PROMH | B4EXV8 from UniProtKB/TrEMBL  Length:343

    Alignment length:363
                                                                                                                                                                                                                                                                                                                                                                                343                    
                                    10        20        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  |      -         -   
         B4EXV8_PROMH     1 MKGYIQTVTGPVKKADMGLTLPHEHLFNDLSGVVDEPFYEFSHVLVDKKVSADIQWGLKYDPYCCCDNMDKKPIEDVIFELNNFKELGGKTIVDATGSSSIGRDIRKLKQVAELTGINVVASSGLYIEKFEGKRLADDIDAMAKMIDDELNIGIDGTDIRAGMIGEIGVSPFFTDGEKNSLRAAALAQNNNPYASMNIHMPGWQRRGDEVLDILLTEMGCDPAKISLAHSDPSGKDIDYQCKMLDRGVWLEFDMIGLDISFPKEGAAPSVMDTVEAVATLIERGYGNQIVLSHDVFLKQMWAKNGGNGWGFVPNVFLSLLAQRGIDKTIIDKLCIDNPANLLA--------------------   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------PTE-3rhgA01 A:12-343                                                                                                                                                                                                                                                                                                                        -------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.hhh.eeeeee.....hhhhh......hhhhhh....hhhhhhhhh.hhhhhhhhhh..hhhhhhhhhhhhhhh.eeeeee...hhhhh.hhhhhhhhhhhhh.eee.ee...hhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.....hhhhhhhhhhhhhhhh......eeee......hhhhhhhhhh.....hhh.eee..hhhhh.hhhhhhhhhhh..eeee................hhhhhhhhhhhhhhh.hhh.eee.....hhhhhhhhh....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rhg A   1 MKGYIQTVTGPVKKADMGLTLPHEHLFNDLSGVVDEPFYEFSHVLVDKKVSADIQWGLKYDPYCCCDNMDKKPIEDVIFELNNFKELGGKTIVDATGSSSIGRDIRKLKQVAELTGINVVASSGLYIEKFEGKRLADDIDAMAKMIDDELNIGIDGTDIRAGMIGEIGVSPFFTDGEKNSLRAAALAQNNNPYASMNIHMPGWQRRGDEVLDILLTEMGCDPAKISLAHSDPSGKDIDYQCKMLDRGVWLEFDMIGLDISFPKEGAAPSVMDTVEAVATLIERGYGNQIVLSHDVFLKQMWAKNGGNGWGFVPNVFLSLLAQRGIDKTIIDKLCIDNPANLLAAENLYFQSHHHHHHWSHPQF 364
                                    10        20        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||     361   
                                                                                                                                                                                                                                                                                                                                                                                        351|           
                                                                                                                                                                                                                                                                                                                                                                                         353
   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 3RHG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Amidohydrolase (126)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (B4EXV8_PROMH | B4EXV8)
molecular function
    GO:0016788    hydrolase activity, acting on ester bonds    Catalysis of the hydrolysis of any ester bond.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0009056    catabolic process    The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism.

 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
    BEZ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CAC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    UNL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ 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 ]
 
  Cis Peptide Bonds
    Gly A:165 - Glu A:166   [ RasMol ]  
 
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
  3rhg
    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
  B4EXV8_PROMH | B4EXV8
    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
  B4EXV8_PROMH | B4EXV8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        B4EXV8_PROMH | B4EXV8: 4qsf

(-) Related Entries Specified in the PDB File

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