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(-) Description

Title :  X-RAY STRUCTURE OF OF HUMAN GLUTAMATE CARBOXYPEPTIDASE II (GCPII) IN A COMPLEX WITH CEIBZL, A UREA-BASED INHIBITOR N~2~-{[(1S)-1-CARBOXYBUT-3-YN-1-YL]CARBAMOYL}-N~6~-(4-IODOBENZOYL)-L-LYSINE
 
Authors :  J. Pavlicek, J. Ptacek, J. Cerny, Y. Byun, L. Skultetyova, M. Pomper, J. Lubkowski, C. Barinka
Date :  08 Jan 14  (Deposition) - 21 May 14  (Release) - 21 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hydrolase, Metallopeptidase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Pavlicek, J. Ptacek, J. Cerny, Y. Byun, L. Skultetyova, M. G. Pomper J. Lubkowski, C. Barinka
Structural Characterization Of P1'-Diversified Urea-Based Inhibitors Of Glutamate Carboxypeptidase Ii.
Bioorg. Med. Chem. Lett. V. 24 2340 2014
PubMed-ID: 24731280  |  Reference-DOI: 10.1016/J.BMCL.2014.03.066

(-) Compounds

Molecule 1 - GLUTAMATE CARBOXYPEPTIDASE 2
    ChainsA
    EC Number3.4.17.21
    EngineeredYES
    Expression SystemDROSOPHILA MELANOGASTER
    Expression System StrainSCHNEIDER'S S2 CELLS
    Expression System Taxid7227
    Expression System Vector TypePLASMID
    GeneFOLH, FOLH1, GIG27, NAALAD1, PSM, PSMA
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCELL 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, PSM, 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, 21)

Asymmetric Unit (8, 21)
No.NameCountTypeFull Name
12QQ1Ligand/IonN~2~-{[(1S)-1-CARBOXYBUT-3-YN-1-YL]CARBAMOYL}-N~6~-(4-IODOBENZOYL)-L-LYSINE
2BMA2Ligand/IonBETA-D-MANNOSE
3CA1Ligand/IonCALCIUM ION
4CL1Ligand/IonCHLORIDE ION
5FUC2Ligand/IonALPHA-L-FUCOSE
6MAN1Ligand/IonALPHA-D-MANNOSE
7NAG11Ligand/IonN-ACETYL-D-GLUCOSAMINE
8ZN2Ligand/IonZINC ION
Biological Unit 1 (5, 34)
No.NameCountTypeFull Name
12QQ2Ligand/IonN~2~-{[(1S)-1-CARBOXYBUT-3-YN-1-YL]CARBAMOYL}-N~6~-(4-IODOBENZOYL)-L-LYSINE
2BMA4Ligand/IonBETA-D-MANNOSE
3CA-1Ligand/IonCALCIUM ION
4CL-1Ligand/IonCHLORIDE ION
5FUC4Ligand/IonALPHA-L-FUCOSE
6MAN2Ligand/IonALPHA-D-MANNOSE
7NAG22Ligand/IonN-ACETYL-D-GLUCOSAMINE
8ZN-1Ligand/IonZINC ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:76 , GLN A:99 , NAG A:802 , HOH A:1131 , HOH A:1158 , HOH A:1351BINDING SITE FOR RESIDUE NAG A 801
02AC2SOFTWARENAG A:801 , HOH A:1138BINDING SITE FOR RESIDUE NAG A 802
03AC3SOFTWAREASN A:121 , THR A:123 , HIS A:124 , THR A:349 , FUC A:804BINDING SITE FOR RESIDUE NAG A 803
04AC4SOFTWARETHR A:123 , HIS A:124 , NAG A:803BINDING SITE FOR RESIDUE FUC A 804
05AC5SOFTWARETYR A:127 , GLU A:137 , ILE A:138 , ASN A:140 , NAG A:806 , FUC A:807BINDING SITE FOR RESIDUE NAG A 805
06AC6SOFTWARENAG A:805 , HOH A:1221BINDING SITE FOR RESIDUE NAG A 806
07AC7SOFTWARENAG A:805BINDING SITE FOR RESIDUE FUC A 807
08AC8SOFTWAREASN A:195 , SER A:197BINDING SITE FOR RESIDUE NAG A 808
09AC9SOFTWARETRP A:246 , ASN A:459 , PHE A:565 , TYR A:566 , HOH A:976 , HOH A:1149 , HOH A:1397 , HOH A:1411BINDING SITE FOR RESIDUE NAG A 809
10BC1SOFTWARESER A:472 , ASN A:476 , PRO A:594 , NAG A:811 , HOH A:1326 , HOH A:1394BINDING SITE FOR RESIDUE NAG A 810
11BC2SOFTWAREGLN A:651 , NAG A:810 , BMA A:812 , HOH A:1395 , HOH A:1406 , HOH A:1407BINDING SITE FOR RESIDUE NAG A 811
12BC3SOFTWAREGLN A:651 , NAG A:811BINDING SITE FOR RESIDUE BMA A 812
13BC4SOFTWARESER A:631 , SER A:634 , ASN A:638 , GLN A:740 , NAG A:814 , HOH A:1024 , HOH A:1056 , HOH A:1206BINDING SITE FOR RESIDUE NAG A 813
14BC5SOFTWARENAG A:813 , BMA A:815BINDING SITE FOR RESIDUE NAG A 814
15BC6SOFTWAREHIS A:112 , GLU A:276 , LYS A:324 , ARG A:354 , NAG A:814 , MAN A:816BINDING SITE FOR RESIDUE BMA A 815
16BC7SOFTWAREPHE A:235 , LYS A:240 , SER A:241 , GLU A:276 , BMA A:815 , HOH A:1083 , HOH A:1204 , HOH A:1207 , HOH A:1283BINDING SITE FOR RESIDUE MAN A 816
17BC8SOFTWAREASP A:387 , GLU A:425 , HIS A:553 , ZN A:818 , 2QQ A:821 , HOH A:1348BINDING SITE FOR RESIDUE ZN A 817
18BC9SOFTWAREHIS A:377 , ASP A:387 , GLU A:424 , GLU A:425 , ASP A:453 , ZN A:817 , HOH A:1348BINDING SITE FOR RESIDUE ZN A 818
19CC1SOFTWARETHR A:269 , TYR A:272 , GLU A:433 , GLU A:436 , HOH A:905BINDING SITE FOR RESIDUE CA A 819
20CC2SOFTWAREASN A:451 , ASP A:453 , ARG A:534 , ARG A:536BINDING SITE FOR RESIDUE CL A 820
21CC3SOFTWAREARG A:210 , ASN A:257 , GLU A:424 , GLU A:425 , ARG A:463 , ASP A:465 , GLY A:518 , ASN A:519 , ARG A:534 , ARG A:536 , PHE A:546 , TYR A:552 , HIS A:553 , TYR A:700 , ZN A:817 , HOH A:908 , HOH A:1065 , HOH A:1348 , HOH A:1349BINDING SITE FOR RESIDUE 2QQ A 821

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4OC2)

(-) 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 4OC2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OC2)

(-) Exons   (0, 0)

(no "Exon" information available for 4OC2)

(-) 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...hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.................eeee..eeeeeeehhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oc2 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 4OC2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4OC2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OC2)

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        FOLH1_HUMAN | Q046091z8l 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 4oc3 4oc4 4oc5 4ome 4p44 4p45 4p4b 4p4d 4p4e 4p4f 4p4i 4p4j 4w9y 4x3r 5d29 5ely 5f09

(-) Related Entries Specified in the PDB File

4oc0 4oc1 4oc3 4oc4 4oc5