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(-) Description

Title :  X-RAY STRUCTURE OF HUMAN GLUTAMATE CARBOXYPEPTIDASE II (GCPII) IN COMPLEX WITH A PHOSPHORAMIDATE INHIBITOR MP1D
 
Authors :  C. Barinka
Date :  12 Mar 14  (Deposition) - 20 May 15  (Release) - 20 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.67
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Glutamate Carboxypeptidase Ii (Gcpii); Naaladase; Prostate-Specific Membrane Antigen; 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 CELLS
    Expression System Common: FRUIT FLY
    Expression System Taxid: 7227
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 44-750
    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 Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 22)

Asymmetric Unit (8, 22)
No.NameCountTypeFull Name
12G41Ligand/IonN-[(S)-HYDROXY(4-PHENYLBUTOXY)PHOSPHORYL]-L-GLUTAMICACID
2BMA2Ligand/IonBETA-D-MANNOSE
3CA1Ligand/IonCALCIUM ION
4CL1Ligand/IonCHLORIDE ION
5FUC2Ligand/IonALPHA-L-FUCOSE
6MAN1Ligand/IonALPHA-D-MANNOSE
7NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE
8ZN2Ligand/IonZINC ION
Biological Unit 1 (5, 36)
No.NameCountTypeFull Name
12G42Ligand/IonN-[(S)-HYDROXY(4-PHENYLBUTOXY)PHOSPHORYL]-L-GLUTAMICACID
2BMA4Ligand/IonBETA-D-MANNOSE
3CA-1Ligand/IonCALCIUM ION
4CL-1Ligand/IonCHLORIDE ION
5FUC4Ligand/IonALPHA-L-FUCOSE
6MAN2Ligand/IonALPHA-D-MANNOSE
7NAG24Ligand/IonN-ACETYL-D-GLUCOSAMINE
8ZN-1Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:387 , GLU A:425 , HIS A:553 , 2G4 A:822binding site for residue ZN A 818
02AC2SOFTWAREHIS A:377 , ASP A:387 , GLU A:425 , ASP A:453 , 2G4 A:822binding site for residue ZN A 819
03AC3SOFTWARETHR A:269 , TYR A:272 , GLU A:433 , GLU A:436 , HOH A:949binding site for residue CA A 820
04AC4SOFTWAREASN A:451 , ASP A:453 , ARG A:534binding site for residue CL A 821
05AC5SOFTWAREARG 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 , GLU A:457 , GLY A:518 , ASN A:519 , LYS A:545 , GLY A:548 , TYR A:549 , TYR A:552 , HIS A:553 , LYS A:699 , TYR A:700 , ZN A:818 , ZN A:819 , HOH A:985 , HOH A:992 , HOH A:1010binding site for residue 2G4 A 822
06AC6SOFTWAREASN A:76 , GLN A:79 , GLN A:99 , HOH A:1194 , HOH A:1404 , HOH A:1430binding 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:124binding site for Poly-Saccharide residues NAG A 803 through FUC A 805 bound to ASN A 121
08AC8SOFTWARETYR A:127 , GLU A:137 , ILE A:138 , ASN A:140 , HOH A:1113binding site for Poly-Saccharide residues NAG A 806 through FUC A 808 bound to ASN A 140
09AC9SOFTWAREASN A:195binding site for Mono-Saccharide NAG A 809 bound to ASN A 195
10AD1SOFTWARETRP A:246 , ASN A:459 , PHE A:565 , TYR A:566 , HOH A:948 , HOH A:1094 , HOH A:1269 , HOH A:1272binding site for Mono-Saccharide NAG A 810 bound to ASN A 459
11AD2SOFTWARESER A:472 , ASN A:476 , PRO A:594 , GLN A:651 , HOH A:1165 , HOH A:1244 , HOH A:1300 , HOH A:1324binding site for Poly-Saccharide residues NAG A 811 through BMA A 813 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:905 , HOH A:911 , HOH A:916 , HOH A:921 , HOH A:1162 , HOH A:1201 , HOH A:1277 , HOH A:1285binding site for Poly-Saccharide residues NAG A 814 through MAN A 817 bound to ASN A 638

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4P4E)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric 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 4P4E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P4E)

(-) Exons   (0, 0)

(no "Exon" information available for 4P4E)

(-) 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:694
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               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...hhhhhhhhhhhh..........hhhhhhhhhh...................hhhhhhh...eeeeeeee..hhhhh............hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh................eeee..eeeeeeehhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p4e A  55 KHNMKAFLDELKAENIKKFLYNFTQIPHLAGTEQNFQLAKQIQSQWKEFGLDSVELAHYDVLLSYPNKTHPNYISIINEDGNEIFNTSLFEPPPPGYENVSDIVPPFSAFSPQGMPEGDLVYVNYARTEDFFKLERDMKINCSGKIVIARYGKVFRGNKVKNAQLAGAKGVILYSDPADYFAPGVKSYPDGWNLPGGGVQRGNILNLNGAGDPLTPGYPANEYAYRRGIAEAVGLPSIPVHPIGYYDAQKLLEKMGGSAPPDSSWRGSLKVPYNVGPGFTGNFSTQKVKMHIHSTNEVTRIYNVIGTLRGAVEPDRYVILGGHRDSWVFGGIDPQSGAAVVHEIVRSFGTLKKEGWRPRRTILFASWDAEEFGLLGSTEWAEENSRLLQERGVAYINADSSIEGNYTLRVDCTPLMYSLVHNLTKELKSPDEGFEGKSLYESWTKKSPSPEFSGMPRISKLGSGNDFEVFFQRLGIASGRARYTKNWETNKFSGYPLYHSVYETYELVEKFYDPMFKYHLTVAQVRGGMVFELANSIVLPFDCRDYAVVLRKYADKIYSISMKHPQEMKTYSVSFDSLFSAVKNFTEIASKFSERLQDFSNPIVLRMMNDQLMFLERAFIDPLGLPDRPFYRHVIYAPSSHNKYAGESFPGIYDALFDIESKVDPSKAWGEVKRQIYVAAFTVQAAAETLSEVA 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       554       564       574       584       594       604       614       624       634       644       656       666       676       686       696       706       716       726       736       746    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                653|                                                                                              
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 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 4P4E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P4E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P4E)

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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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 4p44 4p45 4p4b 4p4d 4p4f 4p4i 4p4j 4w9y 4x3r 5d29 5ely 5f09

(-) Related Entries Specified in the PDB File

4p4b 4p4d 4p4f 4p4i 4p4j