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(-) Description

Title :  CRYSTAL STRUCTURE OF GLUTAMATE CARBOXYPEPTIDASE II IN A COMPLEX WITH UREA-BASED INHIBITOR
 
Authors :  J. Tykvart, P. Pachl
Date :  02 Nov 13  (Deposition) - 18 Jun 14  (Release) - 18 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.08
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hydrolase, Metallopeptidase, Glycoprotein, Urea-Based Inhibitor, Trasmembrane, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Tykvart, J. Schimer, J. Barinkova, P. Pachl, L. Postova-Slavetinska, P. Majer, J. Konvalinka, P. Sacha
Rational Design Of Urea-Based Glutamate Carboxypeptidase Ii (Gcpii) Inhibitors As Versatile Tools For Specific Drug Targeting And Delivery
Bioorg. Med. Chem. 2014
PubMed: search  |  Reference-DOI: 10.1016/J.BMC.2014.05.061

(-) 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 2(S2) CELLS
    Expression System Plasmid: PMT/BIP
    Expression System Taxid: 7227
    Expression System Vector Type: BACULOVIRUS
    Fragment: EXTRACELLULAR DOMAIN, UNP RESIDUES 44-750
    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, 20)

Asymmetric Unit (7, 20)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CA1Ligand/IonCALCIUM ION
3CL1Ligand/IonCHLORIDE ION
4J371Ligand/IonN-({(1S)-6-(4-BROMOBENZYL)-1-CARBOXY-7,47-DIOXO-52-[(3AS,4S,6AR)-2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL]-10,13,16,19,22,25,28,31,34,37,40,43-DODECAOXA-6,46-DIAZADOPENTACONT-1-YL}CARBAMOYL)-L-GLUTAMIC ACID
5MAN2Ligand/IonALPHA-D-MANNOSE
6NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE
7ZN2Ligand/IonZINC ION
Biological Unit 1 (4, 32)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2CA-1Ligand/IonCALCIUM ION
3CL-1Ligand/IonCHLORIDE ION
4J372Ligand/IonN-({(1S)-6-(4-BROMOBENZYL)-1-CARBOXY-7,47-DIOXO-52-[(3AS,4S,6AR)-2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL]-10,13,16,19,22,25,28,31,34,37,40,43-DODECAOXA-6,46-DIAZADOPENTACONT-1-YL}CARBAMOYL)-L-GLUTAMIC ACID
5MAN4Ligand/IonALPHA-D-MANNOSE
6NAG24Ligand/IonN-ACETYL-D-GLUCOSAMINE
7ZN-1Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:377 , ASP A:387 , GLU A:425 , ASP A:453 , ZN A:817 , HOH A:1095BINDING SITE FOR RESIDUE ZN A 816
02AC2SOFTWAREASP A:387 , GLU A:425 , HIS A:553 , ZN A:816 , J37 A:820 , HOH A:1095BINDING SITE FOR RESIDUE ZN A 817
03AC3SOFTWAREASN A:451 , ASP A:453 , ARG A:534 , ARG A:536BINDING SITE FOR RESIDUE CL A 818
04AC4SOFTWARETHR A:269 , TYR A:272 , GLU A:433 , GLU A:436 , HOH A:903BINDING SITE FOR RESIDUE CA A 819
05AC5SOFTWAREARG A:210 , ASN A:257 , ASP A:387 , GLU A:424 , GLU A:425 , GLY A:427 , LEU A:428 , GLU A:457 , ARG A:463 , ASP A:465 , GLY A:518 , ASN A:519 , ARG A:534 , ARG A:536 , TYR A:552 , HIS A:553 , LYS A:699 , TYR A:700 , ZN A:817 , HOH A:907 , HOH A:942 , HOH A:1051 , HOH A:1087 , HOH A:1095BINDING SITE FOR RESIDUE J37 A 820
06AC6SOFTWAREASN A:76 , GLN A:95 , SER A:98 , HOH A:971BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 76 RESIDUES 801 TO 802
07AC7SOFTWAREASN A:121 , THR A:123 , HIS A:124 , THR A:349 , HOH A:1367BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 121 RESIDUES 803 TO 804
08AC8SOFTWARETYR A:127 , GLU A:137 , ILE A:138 , ASN A:140 , HOH A:1125BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 140 RESIDUES 805 TO 806
09AC9SOFTWAREASN A:195 , SER A:197 , HOH A:1350BINDING SITE FOR MONO-SACCHARIDE NAG A 807 BOUND TO ASN A 195
10BC1SOFTWARETRP A:246 , ASN A:459 , PHE A:565 , TYR A:566 , HOH A:1012 , HOH A:1140 , HOH A:1312 , HOH A:1316BINDING SITE FOR MONO-SACCHARIDE NAG A 808 BOUND TO ASN A 459
11BC2SOFTWARESER A:472 , ASN A:476 , PRO A:594 , HOH A:1154 , HOH A:1318BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 476 RESIDUES 809 TO 810
12BC3SOFTWARELEU A:110 , HIS 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:1104 , HOH A:1131 , HOH A:1314BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 638 RESIDUES 811 TO 815

(-) SS Bonds  (0, 0)

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

(-) 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 4NGQ)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NGQ)

(-) 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.......hhhhhhhhhhhhhhhhhh...eeeeeeeeeeeee.......eeeee.....eeee..............................ee.eee....hhhhhhhhhhh........eeeee....hhhhhhhhhhhh...eeeee.hhhhhh..............................................hhhhh.......eeeehhhhhhhhhh........hhhhh.............hhhhh..eeeee...eeeeeeeeeeeeee....eeeeeeeeeee..........hhhhhhhhhhhhhhhhhhhhh.....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhheeeeee.........eeeeee...hhhhhhhhhhh...........hhhhhhhhhh...................hhhhhh....eeeeeeee.................hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh................eeee..eeeeeeehhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ngq A  55 KHNMKAFLDELKAENIKKFLYNFTQIPHLAGTEQNFQLAKQIQSQWKEFGLDSVELAHYDVLLSYPNKTHPNYISIINEDGNEIFNTSLFEPPPPGYENVSDIVPPFSAFSPQGMPEGDLVYVNYARTEDFFKLERDMKINCSGKIVIARYGKVFRGNKVKNAQLAGAKGVILYSDPADYFAPGVKSYPDGWNLPGGGVQRGNILNLNGAGDPLTPGYPANEYAYRRGIAEAVGLPSIPVHPIGYYDAQKLLEKMGGSAPPDSSWRGSLKVPYNVGPGFTGNFSTQKVKMHIHSTNEVTRIYNVIGTLRGAVEPDRYVILGGHRDSWVFGGIDPQSGAAVVHEIVRSFGTLKKEGWRPRRTILFASWDAEEFGLLGSTEWAEENSRLLQERGVAYINADSSIEGNYTLRVDCTPLMYSLVHNLTKELKSPDEGFEGKSLYESWTKKSPSPEFSGMPRISKLGSGNDFEVFFQRLGIASGRARYTKNWETNSGYPLYHSVYETYELVEKFYDPMFKYHLTVAQVRGGMVFELANSIVLPFDCRDYAVVLRKYADKIYSISMKHPQEMKTYSVSFDSLFSAVKNFTEIASKFSERLQDFDKSNPIVLRMMNDQLMFLERAFIDPLGLPDRPFYRHVIYAPSSHNKYAGESFPGIYDALFDIESKVDPSKAWGEVKRQIYVAAFTVQAAAETLSEVA 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|      556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   544|                                                                                                                                                                                                           
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    547
   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 4NGQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 4ngr 4ngs 4ngt 4oc0 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

3d7h 4ngm 4ngn 4ngp 4ngr 4ngs 4ngt