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(-) Description

Title :  X-RAY STRUCTURE OF HUMAN GLUTAMATE CARBOXYPEPTIDASE II (GCPII) IN COMPLEX WITH A HYDROXAMATE INHIBITOR JHU242
 
Authors :  C. Barinka, Z. Novakova, J. Pavlicek
Date :  05 Nov 15  (Deposition) - 27 Apr 16  (Release) - 08 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.81
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Prostate-Specific Membrane Antigen, Naaladase, Phosphoramidate, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Novakova, K. Wozniak, A. Jancarik, R. Rais, Y. Wu, J. Pavlicek, D. Ferraris, B. Havlinova, J. Ptacek, J. Vavra, N. Hin, C. Rojas, P. Majer, B. S. Slusher, T. Tsukamoto, C. Barinka
Unprecedented Binding Mode Of Hydroxamate-Based Inhibitors Of Glutamate Carboxypeptidase Ii: Structural Characterization And Biological Activity.
J. Med. Chem. V. 59 4539 2016
PubMed-ID: 27074627  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B01806

(-) 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
    Fragment: UNP RESIDUES 55-750
    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, 18)

Asymmetric Unit (8, 18)
No.NameCountTypeFull Name
15PU1Ligand/Ion4-[(2~{R})-2-CARBOXY-5-(OXIDANYLAMINO)-5-OXIDANYLIDENE-PENTYL]BENZOIC ACID
2ACT1Ligand/IonACETATE ION
3BMA1Ligand/IonBETA-D-MANNOSE
4CA1Ligand/IonCALCIUM ION
5CL1Ligand/IonCHLORIDE ION
6MAN1Ligand/IonALPHA-D-MANNOSE
7NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE
8ZN2Ligand/IonZINC ION
Biological Unit 1 (5, 28)
No.NameCountTypeFull Name
15PU2Ligand/Ion4-[(2~{R})-2-CARBOXY-5-(OXIDANYLAMINO)-5-OXIDANYLIDENE-PENTYL]BENZOIC ACID
2ACT2Ligand/IonACETATE ION
3BMA2Ligand/IonBETA-D-MANNOSE
4CA-1Ligand/IonCALCIUM ION
5CL-1Ligand/IonCHLORIDE ION
6MAN2Ligand/IonALPHA-D-MANNOSE
7NAG20Ligand/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 , ZN A:802 , 5PU A:817binding site for residue ZN A 801
02AC2SOFTWAREHIS A:377 , ASP A:387 , ASP A:453 , ZN A:801 , 5PU A:817 , HOH A:1126binding site for residue ZN A 802
03AC3SOFTWARETHR A:269 , TYR A:272 , GLU A:433 , GLU A:436 , HOH A:966binding site for residue CA A 803
04AC4SOFTWAREASN A:451 , ASP A:453 , ARG A:534binding site for residue CL A 804
05AC5SOFTWARETYR A:234 , HIS A:377 , ASP A:387 , GLU A:424 , GLU A:425 , 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 , ZN A:801 , ZN A:802 , ACT A:818 , HOH A:1126 , HOH A:1159binding site for residue 5PU A 817
06AC6SOFTWAREARG A:210 , GLU A:425 , TYR A:552 , HIS A:553 , 5PU A:817 , HOH A:1076 , HOH A:1238 , HOH A:1262 , HOH A:1350binding site for residue ACT A 818
07AC7SOFTWAREASN A:76 , GLN A:95 , GLN A:99 , HOH A:911 , HOH A:1087 , HOH A:1246 , HOH A:1265 , HOH A:1307binding site for Poly-Saccharide residues NAG A 805 through NAG A 806 bound to ASN A 76
08AC8SOFTWAREASN A:121 , THR A:123 , HIS A:124 , THR A:349binding site for Mono-Saccharide NAG A 807 bound to ASN A 121
09AC9SOFTWARETYR A:127 , GLU A:137 , ILE A:138 , ASN A:140binding site for Poly-Saccharide residues NAG A 808 through NAG A 809 bound to ASN A 140
10AD1SOFTWARETRP A:246 , ASN A:459 , PHE A:565 , TYR A:566 , HOH A:924 , HOH A:1154 , HOH A:1217 , HOH A:1245binding site for Mono-Saccharide NAG A 810 bound to ASN A 459
11AD2SOFTWARESER A:472 , ASN A:476 , GLN A:651 , HOH A:1150 , HOH A:1267binding site for Poly-Saccharide residues NAG A 811 through NAG A 812 bound to ASN A 476
12AD3SOFTWAREHIS A:112 , PHE A:235 , LYS A:240 , SER A:241 , GLU A:276 , TYR A:277 , ARG A:354 , SER A:631 , SER A:634 , ASN A:638 , GLN A:740 , HOH A:903 , HOH A:916 , HOH A:952 , HOH A:1143 , HOH A:1176 , HOH A:1210binding site for Poly-Saccharide residues NAG A 813 through MAN A 816 bound to ASN A 638

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5ELY)

(-) 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 5ELY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5ELY)

(-) Exons   (0, 0)

(no "Exon" information available for 5ELY)

(-) 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:682
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeee.......eeeee...ee.....................ee.......ee.eee....hhhhhhhhhhh........eeeee....hhhhhhhhhhhh...eeeee.hhhhhh....................ee........................hhhhh.......eeeehhhhhhhhhh........hhhhh.............hhhhh..eeeee...eeeeeeeeeeeeee....eeeeeeeeeee..........hhhhhhhhhhhhhhhhhhhhh.....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhheeeeee.........eeeeee...hhhhhhhhhhh...........hhhhhhhhhh...................hhhhhhh...eeeeeeee...............hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.........................hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ely A  55 KHNMKAFLDELKAENIKKFLYNFTQIPHLAGTEQNFQLAKQIQSQWKEFGLDSVELAHYDVLLSYPNKTHPNYISIINEIFNTSLFEPPPPGYENVSDIVPPFSAFSPQGMPEGDLVYVNYARTEDFFKLERDMKINCSGKIVIARYGKVFRGNKVKNAQLAGAKGVILYSDPADYFAPGVKSYPDGWNLPGGGVQRGNILNLNGAGDPLTPGYPANEYAYRRGIAEAVGLPSIPVHPIGYYDAQKLLEKMGGSAPPDSSWRGSLKVPYNVGPGFTGNFSTQKVKMHIHSTNEVTRIYNVIGTLRGAVEPDRYVILGGHRDSWVFGGIDPQSGAAVVHEIVRSFGTLKKEGWRPRRTILFASWDAEEFGLLGSTEWAEENSRLLQERGVAYINADSSIEGNYTLRVDCTPLMYSLVHNLTKELKSPDEGFEGKSLYESWTKKSPSPEFSGMPRISKLGSGNDFEVFFQRLGIASGRARYTKNWETGYPLYHSVYETYELVEKFYDPMFKYHLTVAQVRGGMVFELANSIVLPFDCRDYAVVLRKYADKIYSISMKHPQEMKTYSVSFDSLFSAVKNFTEIASKFSERLQDFSNPIVLRMMNDQLMFLERAFIDPLGLPDRPFYRHVIYAPSSHNESFPGIYDALFDIESKVDPSKAWGEVKRQIYVAAFTVQAAAETLSEVA 750
                                    64        74        84        94       104       114       124      |138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538    || 552       562       572       582       592       602       612       622       632       642       652||     664       674       684       694   ||  708       718       728       738       748  
                                                                                                      131|                                                                                                                                                                                                                                                                                                                                                                                                                    543|                                                                                                      653|                                       698|                                               
                                                                                                       136                                                                                                                                                                                                                                                                                                                                                                                                                     548                                                                                                       656                                        703
   Legend:   → Mismatch (orange background)
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    → 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 5ELY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5ELY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5ELY)

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

(-) Related Entries Specified in the PDB File

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