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(-) Description

Title :  X-RAY STRUCTURE OF OF HUMAN GLUTAMATE CARBOXYPEPTIDASE II (GCPII) IN A COMPLEX WITH CCIBZL, A UREA-BASED INHIBITOR N~2~-[(1-CARBOXYCYCLOPROPYL)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 :  1.85
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
    Chains: A
    EC Number: 3.4.17.21
    Engineered: YES
    Expression System: DROSOPHILA MELANOGASTER
    Expression System Strain: SCHNEIDER'S S2 CELLS
    Expression System Taxid: 7227
    Expression System Vector Type: PLASMID
    Gene: FOLH, FOLH1, GIG27, NAALAD1, PSM, PSMA
    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, 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  (7, 18)

Asymmetric Unit (7, 18)
No.NameCountTypeFull Name
12R71Ligand/IonN~2~-[(1-CARBOXYCYCLOPROPYL)CARBAMOYL]-N~6~-(4-IODOBENZOYL)-L-LYSINE
2BMA1Ligand/IonBETA-D-MANNOSE
3CA1Ligand/IonCALCIUM ION
4CL1Ligand/IonCHLORIDE ION
5MAN1Ligand/IonALPHA-D-MANNOSE
6NAG11Ligand/IonN-ACETYL-D-GLUCOSAMINE
7ZN2Ligand/IonZINC ION
Biological Unit 1 (4, 28)
No.NameCountTypeFull Name
12R72Ligand/IonN~2~-[(1-CARBOXYCYCLOPROPYL)CARBAMOYL]-N~6~-(4-IODOBENZOYL)-L-LYSINE
2BMA2Ligand/IonBETA-D-MANNOSE
3CA-1Ligand/IonCALCIUM ION
4CL-1Ligand/IonCHLORIDE ION
5MAN2Ligand/IonALPHA-D-MANNOSE
6NAG22Ligand/IonN-ACETYL-D-GLUCOSAMINE
7ZN-1Ligand/IonZINC ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:76 , GLN A:99 , NAG A:802 , HOH A:1131BINDING SITE FOR RESIDUE NAG A 801
02AC2SOFTWARENAG A:801 , HOH A:1138 , HOH A:1325BINDING SITE FOR RESIDUE NAG A 802
03AC3SOFTWAREASN A:121 , THR A:123 , HIS A:124 , THR A:349BINDING SITE FOR RESIDUE NAG A 803
04AC4SOFTWARETYR A:127 , GLU A:137 , ILE A:138 , ASN A:140 , NAG A:805BINDING SITE FOR RESIDUE NAG A 804
05AC5SOFTWARENAG A:804 , HOH A:1234 , HOH A:1323BINDING SITE FOR RESIDUE NAG A 805
06AC6SOFTWAREASN A:195 , SER A:197BINDING SITE FOR RESIDUE NAG A 806
07AC7SOFTWARETRP A:246 , ASN A:459 , PHE A:565 , TYR A:566 , HOH A:977 , HOH A:1151BINDING SITE FOR RESIDUE NAG A 807
08AC8SOFTWARESER A:472 , ASN A:476 , PRO A:594 , NAG A:809BINDING SITE FOR RESIDUE NAG A 808
09AC9SOFTWAREGLN A:651 , NAG A:808 , HOH A:1335BINDING SITE FOR RESIDUE NAG A 809
10BC1SOFTWAREGLU A:276 , SER A:631 , SER A:634 , ASN A:638 , GLN A:740 , NAG A:811 , HOH A:1023 , HOH A:1207BINDING SITE FOR RESIDUE NAG A 810
11BC2SOFTWAREGLU A:276 , NAG A:810 , BMA A:812BINDING SITE FOR RESIDUE NAG A 811
12BC3SOFTWAREHIS A:112 , GLU A:276 , ARG A:354 , NAG A:811 , MAN A:813 , HOH A:1326 , HOH A:1327BINDING SITE FOR RESIDUE BMA A 812
13BC4SOFTWAREPHE A:235 , LYS A:240 , SER A:241 , GLU A:276 , BMA A:812 , HOH A:1083 , HOH A:1205 , HOH A:1321BINDING SITE FOR RESIDUE MAN A 813
14BC5SOFTWAREASP A:387 , GLU A:425 , HIS A:553 , ZN A:815 , 2R7 A:818 , HOH A:1347BINDING SITE FOR RESIDUE ZN A 814
15BC6SOFTWAREHIS A:377 , ASP A:387 , GLU A:424 , GLU A:425 , ASP A:453 , ZN A:814 , HOH A:1347BINDING SITE FOR RESIDUE ZN A 815
16BC7SOFTWARETHR A:269 , TYR A:272 , GLU A:433 , GLU A:436 , HOH A:906BINDING SITE FOR RESIDUE CA A 816
17BC8SOFTWAREASN A:451 , ASP A:453 , ARG A:534 , ARG A:536BINDING SITE FOR RESIDUE CL A 817
18BC9SOFTWAREARG A:210 , GLU A:424 , GLU A:425 , SER A:454 , ARG A:463 , ASP A:465 , GLY A:518 , ASN A:519 , ARG A:534 , ARG A:536 , TYR A:552 , HIS A:553 , TYR A:700 , ZN A:814 , HOH A:909 , HOH A:1347 , HOH A:1348 , HOH A:1349BINDING SITE FOR RESIDUE 2R7 A 818

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4OC0)

(-) 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 4OC0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OC0)

(-) Exons   (0, 0)

(no "Exon" information available for 4OC0)

(-) 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.hhhhhhhhhhhhhhhhhh.................eeee..eeeeeeehhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oc0 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 4OC0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4OC0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OC0)

(-) 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 | 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 4oc1 4oc2 4oc3 4oc4 4oc5 4ome 4p44 4p45 4p4b 4p4d 4p4e 4p4f 4p4i 4p4j 4w9y 4x3r 5d29 5ely 5f09

(-) Related Entries Specified in the PDB File

4oc1 4oc2 4oc3 4oc4 4oc5