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(-) Description

Title :  X-RAY STRUCTURE OF OF HUMAN GLUTAMATE CARBOXYPEPTIDASE II (GCPII) IN A COMPLEX WITH CPIBZL, A UREA-BASED INHIBITOR N~2~-{[(1S)-1-CARBOXY-2-(PYRIDIN-4-YL)ETHYL]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 :  1.66
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
12QN1Ligand/IonN~2~-{[(1S)-1-CARBOXY-2-(PYRIDIN-4-YL)ETHYL]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
12QN2Ligand/IonN~2~-{[(1S)-1-CARBOXY-2-(PYRIDIN-4-YL)ETHYL]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:95 , GLN A:99 , NAG A:802 , HOH A:1113BINDING SITE FOR RESIDUE NAG A 801
02AC2SOFTWARENAG A:801 , HOH A:1249BINDING SITE FOR RESIDUE NAG A 802
03AC3SOFTWAREASN A:121 , THR A:123 , HIS A:124 , THR A:349 , HOH A:1155BINDING 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:804BINDING SITE FOR RESIDUE NAG A 805
06AC6SOFTWAREGLU A:189 , ASN 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:972 , HOH A:1128BINDING 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:808BINDING SITE FOR RESIDUE NAG A 809
10BC1SOFTWARESER A:631 , SER A:634 , ASN A:638 , GLN A:740 , NAG A:811 , HOH A:1017 , HOH A:1046 , HOH A:1171BINDING SITE FOR RESIDUE NAG A 810
11BC2SOFTWARENAG 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:1250 , HOH A:1251BINDING SITE FOR RESIDUE BMA A 812
13BC4SOFTWAREPHE A:235 , LYS A:240 , SER A:241 , GLU A:276 , BMA A:812 , HOH A:1072 , HOH A:1170 , HOH A:1172BINDING SITE FOR RESIDUE MAN A 813
14BC5SOFTWAREASP A:387 , GLU A:425 , HIS A:553 , ZN A:815 , 2QN A:818 , HOH A:1259BINDING 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:1259BINDING 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
18BC9SOFTWAREPHE A:209 , ARG A:210 , ASN A:257 , GLU A:424 , GLU A:425 , LEU A:428 , 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 , LYS A:699 , TYR A:700 , ZN A:814 , HOH A:909 , HOH A:1256 , HOH A:1257 , HOH A:1259 , HOH A:1263BINDING SITE FOR RESIDUE 2QN A 818

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4OC4)

(-) 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 4OC4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OC4)

(-) Exons   (0, 0)

(no "Exon" information available for 4OC4)

(-) 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:690
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               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................hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh................eeee..eeeeeeehhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4oc4 A  55 KHNMKAFLDELKAENIKKFLYNFTQIPHLAGTEQNFQLAKQIQSQWKEFGLDSVELAHYDVLLSYPNKTHPNYISIINEDGNEIFNTSLFEPPPPGYNVSDIVPPFSAFSPQGMPEGDLVYVNYARTEDFFKLERDMKINCSGKIVIARYGKVFRGNKVKNAQLAGAKGVILYSDPADYFAPGVKSYPDGWNLPGGGVQRGNILNLNGAGDPLTPGYPANEYAYRRGIAEAVGLPSIPVHPIGYYDAQKLLEKMGGSAPPDSSWRGSLKVPYNVGPGFTGNFSTQKVKMHIHSTNEVTRIYNVIGTLRGAVEPDRYVILGGHRDSWVFGGIDPQSGAAVVHEIVRSFGTLKKEGWRPRRTILFASWDAEEFGLLGSTEWAEENSRLLQERGVAYINADSSIEGNYTLRVDCTPLMYSLVHNLTKELKSPDEGFEGKSLYESWTKKSPSPEFSGMPRISKLGSGNDFEVFFQRLGIASGRARYTKNNKFSGYPLYHSVYETYELVEKFYDPMFKYHLTVAQVRGGMVFELANSIVLPFDCRDYAVVLRKYADKIYSISMKHPQEMKTYSVSFDSLFSAVKNFTEIASKFSERLQDFSNPIVLRMMNDQLMFLERAFIDPLGLPDRPFYRHVIYAPSSHNKYAGESFPGIYDALFDIESKVDPSKAWGEVKRQIYVAAFTVQAAAETLSEVA 750
                                    64        74        84        94       104       114       124       134       144      |155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535    || 548       558       568       578       588       598       608       618       628       638       648    || 660       670       680       690       700       710       720       730       740       750
                                                                                                                          151|                                                                                                                                                                                                                                                                                                                                                                                                540|                                                                                                          653|                                                                                              
                                                                                                                           153                                                                                                                                                                                                                                                                                                                                                                                                 544                                                                                                           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 4OC4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4OC4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OC4)

(-) 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 4oc0 4oc1 4oc2 4oc3 4oc5 4ome 4p44 4p45 4p4b 4p4d 4p4e 4p4f 4p4i 4p4j 4w9y 4x3r 5d29 5ely 5f09

(-) Related Entries Specified in the PDB File

4oc0 4oc1 4oc2 4oc3 4oc5