Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  X-RAY STRUCTURE OF HUMAN GLUTAMATE CARBOXYPEPTIDASE II (GCPII) IN COMPLEX WITH A HYDROXAMATE INHIBITOR JHU241
 
Authors :  C. Barinka, Z. Novakova, J. Pavlicek
Date :  05 Aug 15  (Deposition) - 27 Apr 16  (Release) - 08 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
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 56-750
    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  (7, 18)

Asymmetric Unit (7, 18)
No.NameCountTypeFull Name
15Q11Ligand/Ion4-[(2~{S})-2-CARBOXY-5-(OXIDANYLAMINO)-5-OXIDANYLIDENE-PENTYL]BENZOIC ACID
2ACT1Ligand/IonACETATE ION
3BMA2Ligand/IonBETA-D-MANNOSE
4CA1Ligand/IonCALCIUM ION
5CL1Ligand/IonCHLORIDE ION
6NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE
7ZN2Ligand/IonZINC ION
Biological Unit 1 (4, 28)
No.NameCountTypeFull Name
15Q12Ligand/Ion4-[(2~{S})-2-CARBOXY-5-(OXIDANYLAMINO)-5-OXIDANYLIDENE-PENTYL]BENZOIC ACID
2ACT2Ligand/IonACETATE ION
3BMA4Ligand/IonBETA-D-MANNOSE
4CA-1Ligand/IonCALCIUM ION
5CL-1Ligand/IonCHLORIDE ION
6NAG20Ligand/IonN-ACETYL-D-GLUCOSAMINE
7ZN-1Ligand/IonZINC ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:387 , GLU A:425 , HIS A:553 , ZN A:814 , 5Q1 A:818binding site for residue ZN A 813
02AC2SOFTWAREHIS A:377 , ASP A:387 , ASP A:453 , ZN A:813 , 5Q1 A:818 , HOH A:974binding site for residue ZN A 814
03AC3SOFTWARETHR A:269 , TYR A:272 , GLU A:433 , GLU A:436 , HOH A:962binding site for residue CA A 815
04AC4SOFTWAREASN A:451 , ASP A:453 , ARG A:534 , ARG A:536binding site for residue CL A 816
05AC5SOFTWAREPHE A:209 , ARG A:210 , GLU A:425 , TYR A:552 , HIS A:553 , TYR A:700 , 5Q1 A:818 , HOH A:918binding site for residue ACT A 817
06AC6SOFTWARETYR 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 , TYR A:700 , ZN A:813 , ZN A:814 , ACT A:817 , HOH A:920 , HOH A:926 , HOH A:974binding site for residue 5Q1 A 818
07AC7SOFTWAREASN A:76 , GLN A:95 , GLN A:99 , HOH A:1077binding site for Poly-Saccharide residues NAG A 801 through NAG A 802 bound to ASN A 76
08AC8SOFTWAREASN A:121 , THR A:123 , HIS A:124 , THR A:349binding site for Mono-Saccharide NAG A 803 bound to ASN A 121
09AC9SOFTWARETYR A:127 , GLU A:137 , ILE A:138 , ASN A:140binding site for Mono-Saccharide NAG A 804 bound to ASN A 140
10AD1SOFTWAREASN A:195 , SER A:197binding site for Mono-Saccharide NAG A 805 bound to ASN A 195
11AD2SOFTWARETRP A:246 , ASN A:459 , PHE A:565 , TYR A:566 , HOH A:991 , HOH A:1079 , HOH A:1107binding site for Mono-Saccharide NAG A 806 bound to ASN A 459
12AD3SOFTWARESER A:472 , ASN A:476 , PRO A:594 , HOH A:1187binding site for Poly-Saccharide residues NAG A 807 through NAG A 808 bound to ASN A 476
13AD4SOFTWAREHIS A:112 , SER A:241 , GLU A:276 , TYR A:277 , LYS A:324 , ARG A:354 , SER A:631 , SER A:634 , ASN A:638 , GLN A:740 , HOH A:907 , HOH A:908 , HOH A:913 , HOH A:1112 , HOH A:1125 , HOH A:1192binding site for Poly-Saccharide residues NAG A 809 through BMA A 812 bound to ASN A 638

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D29)

(-) 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 5D29)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D29)

(-) Exons   (0, 0)

(no "Exon" information available for 5D29)

(-) 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:686
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               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...hhhhhhhhhhh...........hhhhhhhhhh...................hhhhhh....eeeeeeee.............hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh................eeee..eeeeeeehhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d29 A  56 HNMKAFLDELKAENIKKFLYNFTQIPHLAGTEQNFQLAKQIQSQWKEFGLDSVELAHYDVLLSYPNKTHPNYISIINEDGNEIFNTSLFEPPPPGYENVSDIVPPFSAFSPQGMPEGDLVYVNYARTEDFFKLERDMKINCSGKIVIARYGKVFRGNKVKNAQLAGAKGVILYSDPADYFAPGVKSYPDGWNLPGGGVQRGNILNLNGAGDPLTPGYPANEYAYRRGIAEAVGLPSIPVHPIGYYDAQKLLEKMGGSAPPDSSWRGSLKVPYNVGPGFTGNFSTQKVKMHIHSTNEVTRIYNVIGTLRGAVEPDRYVILGGHRDSWVFGGIDPQSGAAVVHEIVRSFGTLKKEGWRPRRTILFASWDAEEFGLLGSTEWAEENSRLLQERGVAYINADSSIEGNYTLRVDCTPLMYSLVHNLTKELKSPDEGFEGKSLYESWTKKSPSPEFSGMPRISKLGSGNDFEVFFQRLGIASGRARYTKNWGYPLYHSVYETYELVEKFYDPMFKYHLTVAQVRGGMVFELANSIVLPFDCRDYAVVLRKYADKIYSISMKHPQEMKTYSVSFDSLFSAVKNFTEIASKFSERLQDFNPIVLRMMNDQLMFLERAFIDPLGLPDRPFYRHVIYAPSSHNKYAGESFPGIYDALFDIESKVDPSKAWGEVKRQIYVAAFTVQAAAETLSEVA 750
                                    65        75        85        95       105       115       125       135       145       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     ||551       561       571       581       591       601       611       621       631       641       651 ||    664       674       684       694       704       714       724       734       744      
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               541|                                                                                                      653|                                                                                             
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                548                                                                                                       657
   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 5D29)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D29)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D29)

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    5Q1  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    BMA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
    AD4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp A:387 - Pro A:388   [ RasMol ]  
    Gly A:330 - Pro A:331   [ RasMol ]  
    Tyr A:242 - Pro A:243   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5d29
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  FOLH1_HUMAN | Q04609
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.17.21
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  FOLH1_HUMAN | Q04609
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 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 5ely 5f09

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5D29)