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 :  SUBSTRATE BOUND PHOSPHOSERINE PHOSPHATASE COMPLEX STRUCTURE
 
Authors :  W. Wang, H. S. Cho, R. Kim, J. Jancarik, H. Yokota, H. H. Nguyen, I. V. Grigoriev, D. E. Wemmer, S. H. Kim, Berkeley Structural Genomics Center (Bsgc)
Date :  16 Mar 02  (Deposition) - 19 Jun 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Rossmann Fold, Beta-Hairpin, Four-Helix Bundle, Structural Genomics, Bsgc Structure Funded By Nih, Protein Structure Initiative, Psi, Berkeley Structural Genomics Center, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Wang, H. S. Cho, R. Kim, J. Jancarik, H. Yokota, H. H. Nguyen, I. V. Grigoriev, D. E. Wemmer, S. H. Kim
Structural Characterization Of The Reaction Pathway In Phosphoserine Phosphatase: Crystallographic "Snapshots" Of Intermediate States.
J. Mol. Biol. V. 319 421 2002
PubMed-ID: 12051918  |  Reference-DOI: 10.1016/S0022-2836(02)00324-8
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOSERINE PHOSPHATASE
    Chains: A, B
    EC Number: 3.1.3.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: B834(DE3)/PSJS1244
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190
    Synonym: PSP, O-PHOSPHOSERINE PHOSPHOHYDROLASE, PSPASE

 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  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2PO42Ligand/IonPHOSPHATE ION
3SEP2Mod. ResiduePHOSPHOSERINE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
2PO4-1Ligand/IonPHOSPHATE ION
3SEP1Mod. ResiduePHOSPHOSERINE
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
2PO42Ligand/IonPHOSPHATE ION
3SEP1Mod. ResiduePHOSPHOSERINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU B:583 , ARG B:622 , ARG B:704 , LYS B:708 , HOH B:833 , HOH B:954 , HOH B:969BINDING SITE FOR RESIDUE PO4 B 230
2AC2SOFTWAREARG B:591 , LYS B:626 , THR B:631 , HOH B:945 , HOH B:946 , HOH B:951BINDING SITE FOR RESIDUE PO4 B 240
3AC3SOFTWAREASN B:511 , PHE B:512 , ASP B:513 , GLU B:520 , MSE B:543 , PHE B:549 , ARG B:556 , SER B:599 , GLY B:600 , LYS B:644 , ASN B:670 , HOH B:828 , HOH B:933BINDING SITE FOR RESIDUE SEP B 270
4AC4SOFTWAREASN A:11 , PHE A:12 , ASP A:13 , GLU A:20 , THR A:39 , MSE A:43 , PHE A:49 , ARG A:56 , SER A:99 , GLY A:100 , LYS A:144 , ASN A:170 , HOH A:812 , HOH A:815 , HOH A:844BINDING SITE FOR RESIDUE SEP A 770

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1L7P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1L7P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1L7P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1L7P)

(-) Exons   (0, 0)

(no "Exon" information available for 1L7P)

(-) 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:208
 aligned with SERB_METJA | Q58989 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:208
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203        
           SERB_METJA     4 KKKLILFDFDSTLVNNETIDEIAREAGVEEEVKKITKEAMEGKLNFEQSLRKRVSLLKDLPIEKVEKAIKRITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVKDGKLTGDVEGEVLKENAKGEILEKIAKIEGINLEDTVAVGDGANDISMFKKAGLKIAFCAKPILKEKADICIEKRDLREILKYIK 211
               SCOP domains d1l7pa_ A: Phosphoserine phosphatase                                                                                                                                                                             SCOP domains
               CATH domains 1l7pA01      1l7pA02 A:17-77 Phosphoserine phosphatase; domain 2          1l7pA01 A:4-16,A:78-209  [code=3.40.50.1000, no name defined]                                                                       -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.........hhhhhhhhhh.hhhhhhhhhhhhhh...hhhhhhhhhhhh....hhhhhhhhhhh.....hhhhhhhhhhhh.eeeeeeeeeehhhhhhhhhhhh..eeeeeeeeee..eeeeeee......hhhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhh.eeeee..hhhhhh...eee...hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1l7p A   4 KKKLILFNFDSTLVNNETIDEIAREAGVEEEVKKITKEAmEGKLNFEQSLRKRVSLLKDLPIEKVEKAIKRITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVKDGKLTGDVEGEVLKENAKGEILEKIAKIEGINLEDTVAVGDGANDISmFKKAGLKIAFCAKPILKEKADICIEKRDLREILKYIK 211
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173|      183       193       203        
                                                                  43-MSE                                                                                                                            174-MSE                                 


Chain B from PDB  Type:PROTEIN  Length:210
 aligned with SERB_METJA | Q58989 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:210
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
           SERB_METJA     2 EKKKKLILFDFDSTLVNNETIDEIAREAGVEEEVKKITKEAMEGKLNFEQSLRKRVSLLKDLPIEKVEKAIKRITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVKDGKLTGDVEGEVLKENAKGEILEKIAKIEGINLEDTVAVGDGANDISMFKKAGLKIAFCAKPILKEKADICIEKRDLREILKYIK 211
               SCOP domains d1l7pb_ B: Phosphoserine phosphatase                                                                                                                                                                               SCOP domains
               CATH domains 1l7pB01        1l7pB02 B:517-577 Phosphoserine phosphatase; domain 2        1l7pB01 B:502-516,B:578-709  [code=3.40.50.1000, no name defined]                                                                   -- CATH domains
           Pfam domains (1) ---Hydrolase-1l7pB01 B:505-679                                                                                                                                                    -------------------------------- Pfam domains (1)
           Pfam domains (2) ---Hydrolase-1l7pB02 B:505-679                                                                                                                                                    -------------------------------- Pfam domains (2)
         Sec.struct. author .....eeee.........hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh....hhhhhhhhhhh.....hhhhhhhhhhhh..eeeeeeeeehhhhhhhhhhhh..eeeeeeeeee..eeeeeee......hhhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhh.eeeee..hhhhhh...eee...hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1l7p B 502 EKKKKLILFNFDSTLVNNETIDEIAREAGVEEEVKKITKEAmEGKLNFEQSLRKRVSLLKDLPIEKVEKAIKRITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVKDGKLTGDVEGEVLKENAKGEILEKIAKIEGINLEDTVAVGDGANDISmFKKAGLKIAFCAKPILKEKADICIEKRDLREILKYIK 711
                                   511       521       531       541 |     551       561       571       581       591       601       611       621       631       641       651       661       671  |    681       691       701       711
                                                                   543-MSE                                                                                                                            674-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  (1, 2)

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

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: HAD (186)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SERB_METJA | Q58989)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0004647    phosphoserine phosphatase activity    Catalysis of the reaction: L(or D)-O-phosphoserine + H2O = L(or D)-serine + phosphate.
biological process
    GO:0006564    L-serine biosynthetic process    The chemical reactions and pathways resulting in the formation of L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid.
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SEP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1l7p)
 
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
  1l7p
    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
  SERB_METJA | Q58989
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.1.3.3
    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
  SERB_METJA | Q58989
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SERB_METJA | Q58989: 1f5s 1j97 1l7m 1l7n 1l7o

(-) Related Entries Specified in the PDB File

1j97 PSP-BEF3 COMPLEX STRUCTRE
1l7m HIGH RESOLUTION LIGANDED STRUCTURE OF PHOSPHOSERINE PHOSPHATASE (PI COMPLEX)
1l7n TRANSITION STATE ANALOGUE OF PHOSPHOSERINE PHOSPHATASE (ALUMINUM FLUORIDE COMPLEX)
1l7o CRYSTAL STRUCTURE OF PHOSPHOSERINE PHOSPHATASE IN APO FORM RELATED ID: BSGCAIR30380 RELATED DB: TARGETDB