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 :  X-RAY STRUCTURE OF HUMAN GLUTAMATE CARBOXYPEPTIDASE II (GCPII) IN COMPLEX WITH A PHOSPHORAMIDATE INHIBITOR JRB-4-81
 
Authors :  Z. Novakova, C. Barinka
Date :  11 Mar 14  (Deposition) - 20 May 15  (Release) - 20 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Prostate-Specific Membrane Antigen, Naaladase, Phosphoramidate, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Novakova, J. Cerny, C. J. Choy, J. R. Nedrow, J. K. Choi, J. Lubkowski C. E. Berkman, C. Barinka
Design Of Composite Inhibitors Targeting Glutamate Carboxypeptidase Ii: The Importance Of Effector Functionalities.
Febs J. V. 283 130 2016
PubMed-ID: 26460595  |  Reference-DOI: 10.1111/FEBS.13557

(-) Compounds

Molecule 1 - GLUTAMATE CARBOXYPEPTIDASE 2
    Chains: A
    EC Number: 3.4.17.21
    Engineered: YES
    Expression System: DROSOPHILA MELANOGASTER
    Expression System Cell Line: SCHNEIDER'S S2
    Expression System Common: FRUIT FLY
    Expression System Taxid: 7227
    Expression System Vector Type: PLASMID
    Gene: FOLH1, FOLH, NAALAD1, PSM, PSMA, GIG27
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CELL GROWTH-INHIBITING GENE 27 PROTEIN, FOLATE HYDROLASE 1, FOLYLPOLY-GAMMA-GLUTAMATE CARBOXYPEPTIDASE, FGCP, GLUTAMATE CARBOXYPEPTIDASE II, GCPII, MEMBRANE GLUTAMATE CARBOXYPEPTIDASE, MGCP, N-ACETYLATED-ALPHA-LINKED ACIDIC DIPEPTIDASE I, NAALADASE I, PROSTATE-SPECIFIC MEMBRANE ANTIGEN, PSMA, PTEROYLPOLY-GAMMA-GLUTAMATE CARBOXYPEPTIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 18)

Asymmetric/Biological Unit (7, 18)
No.NameCountTypeFull Name
12F71Ligand/IonN-(4-FLUOROBENZOYL)-L-ALLOISOLEUCYL-O-[(S)-{[(1S)-1,3-DICARBOXYPROPYL]AMINO}(HYDROXY)PHOSPHORYL]-L-SERINE
2BMA1Ligand/IonBETA-D-MANNOSE
3CA1Ligand/IonCALCIUM ION
4CL1Ligand/IonCHLORIDE ION
5MAN1Ligand/IonALPHA-D-MANNOSE
6NAG11Ligand/IonN-ACETYL-D-GLUCOSAMINE
7ZN2Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:387 , GLU A:425 , HIS A:553 , ZN A:815 , 2F7 A:818binding site for residue ZN A 814
02AC2SOFTWAREHIS A:377 , ASP A:387 , GLU A:425 , ASP A:453 , ZN A:814 , 2F7 A:818binding site for residue ZN A 815
03AC3SOFTWARETHR A:269 , TYR A:272 , GLU A:433 , GLU A:436 , HOH A:1016binding site for residue CA A 816
04AC4SOFTWAREASN A:451 , ASP A:453 , ARG A:534 , ARG A:536binding site for residue CL A 817
05AC5SOFTWAREGLY A:206 , LYS A:207 , VAL A:208 , ARG A:210 , ASN A:257 , HIS A:377 , ASP A:387 , GLU A:424 , GLU A:425 , GLY A:427 , LEU A:428 , ASP A:453 , GLY A:518 , ASN A:519 , ARG A:534 , ARG A:536 , GLY A:548 , TYR A:549 , TYR A:552 , HIS A:553 , LYS A:699 , TYR A:700 , ZN A:814 , ZN A:815 , HOH A:1019 , HOH A:1151 , HOH A:1491binding site for residue 2F7 A 818
06AC6SOFTWAREASN A:76 , GLN A:99 , HOH A:1205 , HOH A:1212 , HOH A:1231 , HOH A:1428binding site for Poly-Saccharide residues NAG A 801 through NAG A 802 bound to ASN A 76
07AC7SOFTWAREASN A:121 , THR A:123 , HIS A:124 , THR A:349 , HOH A:1258binding site for Mono-Saccharide NAG A 803 bound to ASN A 121
08AC8SOFTWARETYR A:127 , GLU A:137 , ILE A:138 , ASN A:140 , HOH A:1392 , HOH A:1453binding site for Poly-Saccharide residues NAG A 804 through NAG A 805 bound to ASN A 140
09AC9SOFTWAREASN A:195 , SER A:197 , HOH A:1473binding site for Mono-Saccharide NAG A 806 bound to ASN A 195
10AD1SOFTWARETRP A:246 , ASN A:459 , PHE A:565 , TYR A:566 , HOH A:1070 , HOH A:1221 , HOH A:1307binding site for Mono-Saccharide NAG A 807 bound to ASN A 459
11AD2SOFTWARESER A:472 , ASN A:476 , PRO A:594 , HOH A:1184 , HOH A:1265 , HOH A:1479binding site for Poly-Saccharide residues NAG A 808 through NAG A 809 bound to ASN A 476
12AD3SOFTWAREHIS A:112 , PHE A:235 , LYS A:240 , SER A:241 , GLU A:276 , ARG A:354 , SER A:631 , SER A:634 , ASN A:638 , GLN A:740 , HOH A:904 , HOH A:905 , HOH A:909 , HOH A:961 , HOH A:973 , HOH A:985 , HOH A:990 , HOH A:1112 , HOH A:1455binding site for Poly-Saccharide residues NAG A 810 through MAN A 813 bound to ASN A 638

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4P44)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Tyr A:242 -Pro A:243
2Gly A:330 -Pro A:331
3Asp A:387 -Pro A:388

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4P44)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P44)

(-) Exons   (0, 0)

(no "Exon" information available for 4P44)

(-) 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:691
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeee.......eeeee.....eeee.....................ee.......ee.eee....hhhhhhhhhhh........eeeee....hhhhhhhhhhhh...eeeee.hhhhhh....................ee........................hhhhh.......eeeehhhhhhhhhh........hhhhh.............hhhhh..eeeee...eeeeeeeeeeeeee....eeeeeeeeeee..........hhhhhhhhhhhhhhhhhhhhh.....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhheeeeee.........eeeeee...hhhhhhhhhhh...........hhhhhhhhhh..................hhhhhhh....eeeeeeee.hhhhh..........hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.................eeee..eeeeeeehhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p44 A  55 KHNMKAFLDELKAENIKKFLYNFTQIPHLAGTEQNFQLAKQIQSQWKEFGLDSVELAHYDVLLSYPNKTHPNYISIINEDGNEIFNTSLFEPPPPGYENVSDIVPPFSAFSPQGMPEGDLVYVNYARTEDFFKLERDMKINCSGKIVIARYGKVFRGNKVKNAQLAGAKGVILYSDPADYFAPGVKSYPDGWNLPGGGVQRGNILNLNGAGDPLTPGYPANEYAYRRGIAEAVGLPSIPVHPIGYYDAQKLLEKMGGSAPPDSSWRGSLKVPYNVGPGFTGNFSTQKVKMHIHSTNEVTRIYNVIGTLRGAVEPDRYVILGGHRDSWVFGGIDPQSGAAVVHEIVRSFGTLKKEGWRPRRTILFASWDAEEFGLLGSTEWAEENSRLLQERGVAYINADSSIEGNYTLRVDCTPLMYSLVHNLTKELKSPDEGFEGKSLYESWTKKSPSPEFSGMPRISKLGSGNDFEVFFQRLGIASGRARYTKNWETNGYPLYHSVYETYELVEKFYDPMFKYHLTVAQVRGGMVFELANSIVLPFDCRDYAVVLRKYADKIYSISMKHPQEMKTYSVSFDSLFSAVKNFTEIASKFSERLQDFSNPIVLRMMNDQLMFLERAFIDPLGLPDRPFYRHVIYAPSSHNKYAGESFPGIYDALFDIESKVDPSKAWGEVKRQIYVAAFTVQAAAETLSEVA 750
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544|      557       567       577       587       597       607       617       627       637       647     ||659       669       679       689       699       709       719       729       739       749 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   544|                                                                                                      653|                                                                                              
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    548                                                                                                       656
   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 4P44)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P44)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P44)

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    2F7  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    BMA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MAN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ 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 ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp A:387 - Pro A:388   [ RasMol ]  
    Gly A:330 - Pro A:331   [ RasMol ]  
    Tyr A:242 - Pro A:243   [ RasMol ]  
 

(-) 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
  4p44
    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
  FOLH1_HUMAN | Q04609
    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)
  3.4.17.21
    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
  FOLH1_HUMAN | Q04609
    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
        FOLH1_HUMAN | Q04609: 1z8l 2c6c 2c6g 2c6p 2cij 2jbj 2jbk 2oot 2or4 2pvv 2pvw 2xef 2xeg 2xei 2xej 3bhx 3bi0 3bi1 3bxm 3d7d 3d7f 3d7g 3d7h 3iww 3rbu 3sje 3sjf 3sjg 3sjx 4jyw 4jz0 4lqg 4mcp 4mcq 4mcr 4mcs 4ngm 4ngn 4ngp 4ngq 4ngr 4ngs 4ngt 4oc0 4oc1 4oc2 4oc3 4oc4 4oc5 4ome 4p45 4p4b 4p4d 4p4e 4p4f 4p4i 4p4j 4w9y 4x3r 5d29 5ely 5f09

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4P44)