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
(-)Biological Unit 2
(-)Biological Unit 3
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ARGINASE-2 COMPLEXED WITH INHIBITOR 11D: {(5R)-5-AMINO-5-CARBOXY-5-[(3-ENDO)-8-(3,4-DICHLOROBENZYL)-8-AZABICYCLO[3.2.1]OCT-3-YL]PENTYL}(TRIHYDROXY)BORATE(1-)
 
Authors :  A. Cousido-Siah, A. Mitschler, F. X. Ruiz, D. Whitehouse, P. Beckett, M Zandt, M. K. Ji, T. Ryder, R. Jagdmann, M. Andreoli, J. Olczak, M. Mazur W. Czestkowski, W. Piotrowska, H. Schroeter, A. Golebiowski, A. Podj
Date :  28 Jan 13  (Deposition) - 11 Dec 13  (Release) - 11 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Metalloenzyme, Alpha/Beta Fold, Hydrolase, Arginine Metabolism, Manganese, Boronate, Mitochondrion, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Golebiowski, D. Whitehouse, R. P. Beckett, M. Van Zandt, M. K. Ji, T. R. Ryder, E. Jagdmann, M. Andreoli, Y. Lee, R. Sheeler, B. Conway, J. Olczak, M. Mazur, W. Czestkowski, W. Piotrowska, A. Cousido-Siah, F. X. Ruiz, A. Mitschler, A. Podjarny, H. Schroeter
Synthesis Of Quaternary Alpha-Amino Acid-Based Arginase Inhibitors Via The Ugi Reaction.
Bioorg. Med. Chem. Lett. V. 23 4837 2013
PubMed-ID: 23886684  |  Reference-DOI: 10.1016/J.BMCL.2013.06.092

(-) Compounds

Molecule 1 - ARGINASE-2, MITOCHONDRIAL
    ChainsA, B, C
    EC Number3.5.3.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET23B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneARG2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymKIDNEY-TYPE ARGINASE, NON-HEPATIC ARGINASE, TYPE II ARGINASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A  
Biological Unit 2 (1x) B 
Biological Unit 3 (1x)  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 18)

Asymmetric Unit (4, 18)
No.NameCountTypeFull Name
138I3Ligand/Ion{(5R)-5-AMINO-5-CARBOXY-5-[(3-ENDO)-8-(3,4-DICHLOROBENZYL)-8-AZABICYCLO[3.2.1]OCT-3-YL]PENTYL}(TRIHYDROXY)BORATE(1-)
2BEN3Ligand/IonBENZAMIDINE
3BME6Ligand/IonBETA-MERCAPTOETHANOL
4MN6Ligand/IonMANGANESE (II) ION
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
138I1Ligand/Ion{(5R)-5-AMINO-5-CARBOXY-5-[(3-ENDO)-8-(3,4-DICHLOROBENZYL)-8-AZABICYCLO[3.2.1]OCT-3-YL]PENTYL}(TRIHYDROXY)BORATE(1-)
2BEN1Ligand/IonBENZAMIDINE
3BME2Ligand/IonBETA-MERCAPTOETHANOL
4MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
138I1Ligand/Ion{(5R)-5-AMINO-5-CARBOXY-5-[(3-ENDO)-8-(3,4-DICHLOROBENZYL)-8-AZABICYCLO[3.2.1]OCT-3-YL]PENTYL}(TRIHYDROXY)BORATE(1-)
2BEN1Ligand/IonBENZAMIDINE
3BME2Ligand/IonBETA-MERCAPTOETHANOL
4MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 3 (3, 4)
No.NameCountTypeFull Name
138I1Ligand/Ion{(5R)-5-AMINO-5-CARBOXY-5-[(3-ENDO)-8-(3,4-DICHLOROBENZYL)-8-AZABICYCLO[3.2.1]OCT-3-YL]PENTYL}(TRIHYDROXY)BORATE(1-)
2BEN1Ligand/IonBENZAMIDINE
3BME2Ligand/IonBETA-MERCAPTOETHANOL
4MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:120 , ASP A:143 , ASP A:147 , ASP A:251 , MN A:402 , 38I A:406BINDING SITE FOR RESIDUE MN A 401
02AC2SOFTWAREASP A:143 , HIS A:145 , ASP A:251 , ASP A:253 , MN A:401 , 38I A:406BINDING SITE FOR RESIDUE MN A 402
03AC3SOFTWAREASN A:83 , ASN A:84 , LEU A:85 , PRO A:151 , LEU A:152 , THR A:153 , THR A:154BINDING SITE FOR RESIDUE BEN A 403
04AC4SOFTWARELEU A:58 , PHE A:323BINDING SITE FOR RESIDUE BME A 404
05AC5SOFTWAREHIS A:133 , CYS A:134 , SER A:290BINDING SITE FOR RESIDUE BME A 405
06AC6SOFTWARELEU A:81 , HIS A:120 , ASP A:143 , HIS A:145 , ASP A:147 , ASN A:149 , SER A:156 , HIS A:160 , ASP A:202 , ASP A:251 , ASP A:253 , THR A:265 , GLU A:296 , MN A:401 , MN A:402 , HOH A:503 , HOH A:526 , HOH A:531 , HOH A:544 , HOH A:643 , HOH A:659 , HOH A:671BINDING SITE FOR RESIDUE 38I A 406
07AC7SOFTWAREHIS B:120 , ASP B:143 , ASP B:147 , ASP B:251 , MN B:402 , 38I B:406BINDING SITE FOR RESIDUE MN B 401
08AC8SOFTWAREASP B:143 , HIS B:145 , ASP B:251 , ASP B:253 , MN B:401 , 38I B:406BINDING SITE FOR RESIDUE MN B 402
09AC9SOFTWAREASN B:83 , ASN B:84 , LEU B:85 , PRO B:151 , LEU B:152 , THR B:153 , THR B:154BINDING SITE FOR RESIDUE BEN B 403
10BC1SOFTWARECYS B:63 , PHE B:323BINDING SITE FOR RESIDUE BME B 404
11BC2SOFTWAREASP A:136 , CYS B:134 , HOH B:552 , HOH B:568 , HOH B:767BINDING SITE FOR RESIDUE BME B 405
12BC3SOFTWARELEU B:81 , HIS B:120 , ASP B:143 , HIS B:145 , ASP B:147 , ASN B:149 , SER B:155 , SER B:156 , HIS B:160 , ASP B:202 , ASP B:251 , ASP B:253 , THR B:265 , GLU B:296 , MN B:401 , MN B:402 , HOH B:502 , HOH B:505 , HOH B:532 , HOH B:533 , HOH B:548 , HOH B:677 , HOH B:689BINDING SITE FOR RESIDUE 38I B 406
13BC4SOFTWAREASP C:143 , HIS C:145 , ASP C:251 , ASP C:253 , MN C:402 , 38I C:406BINDING SITE FOR RESIDUE MN C 401
14BC5SOFTWAREHIS C:120 , ASP C:143 , ASP C:147 , ASP C:251 , MN C:401 , 38I C:406BINDING SITE FOR RESIDUE MN C 402
15BC6SOFTWAREASN C:83 , ASN C:84 , LEU C:85 , PRO C:151 , LEU C:152 , THR C:153 , THR C:154BINDING SITE FOR RESIDUE BEN C 403
16BC7SOFTWAREHIS C:24 , VAL C:26 , LEU C:58 , CYS C:63 , PHE C:323BINDING SITE FOR RESIDUE BME C 404
17BC8SOFTWAREVAL C:107 , HIS C:130 , HIS C:133 , PRO C:135BINDING SITE FOR RESIDUE BME C 405
18BC9SOFTWARELEU C:81 , HIS C:120 , ASP C:143 , HIS C:145 , ASP C:147 , ASN C:149 , SER C:156 , HIS C:160 , ASP C:202 , ASP C:251 , ASP C:253 , THR C:265 , GLU C:296 , MN C:401 , MN C:402 , HOH C:501 , HOH C:513 , HOH C:522 , HOH C:539 , HOH C:602 , HOH C:633 , HOH C:634BINDING SITE FOR RESIDUE 38I C 406

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:117 -Gly A:118
2Gly B:117 -Gly B:118
3Gly C:117 -Gly C:118

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4IXU)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IXU)

(-) 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:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4ixua_ A: Arginase                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee.........hhhhhhhhhhhhhhhhhhhhh..eeeeeee.................hhhhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhh...eeeee...............hhhhhhhhhhhhhhhhhh.............hhh.eeeeee...hhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhhh.....eeeeee.hhh................hhhhhhhhhhhhhhh..eeeeeee..hhhhh.hhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ixu A  24 HSVAVIGAPFSQGQKRKGVEHGPAAIREAGLMKRLSSLGCHLKDFGDLSFTPVPKDDLYNNLIVNPRSVGLANQELAEVVSRAVSDGYSCVTLGGDHSLAIGTISGHARHCPDLCVVWVDAHADINTPLTTSSGNLHGQPVSFLLRELQDKVPQLPGFSWIKPCISSASIVYIGLRDVDPPEHFILKNYDIQYFSMRDIDRLGIQKVMERTFDLLIGKRQRPIHLSFDIDAFDPTLAPATGTPVVGGLTYREGMYIAEEIHNTGLLSALDLVEVNPQLATSEEEAKTTANLAVDVIASSFGQTREG 329
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323      

Chain B from PDB  Type:PROTEIN  Length:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4ixub_ B: Arginase                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee..........hhhhhhhhhhhhhhhhhhhhh..eeeeeee.................hhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh...eeeee...............hhhhhhhhhhhhhhhhhh.............hhh.eeeeee...hhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhhh.....eeeeee.hhh................hhhhhhhhhhhhhhh..eeeeeee..hhhhh.hhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ixu B  24 HSVAVIGAPFSQGQKRKGVEHGPAAIREAGLMKRLSSLGCHLKDFGDLSFTPVPKDDLYNNLIVNPRSVGLANQELAEVVSRAVSDGYSCVTLGGDHSLAIGTISGHARHCPDLCVVWVDAHADINTPLTTSSGNLHGQPVSFLLRELQDKVPQLPGFSWIKPCISSASIVYIGLRDVDPPEHFILKNYDIQYFSMRDIDRLGIQKVMERTFDLLIGKRQRPIHLSFDIDAFDPTLAPATGTPVVGGLTYREGMYIAEEIHNTGLLSALDLVEVNPQLATSEEEAKTTANLAVDVIASSFGQTREG 329
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323      

Chain C from PDB  Type:PROTEIN  Length:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4ixuc_ C: Arginase                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee..........hhhhhhhhhhhhhhhhhhhhh..eeeeeee.................hhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh...eeeee...............hhhhhhhhhhhhhhhhhh.............hhh.eeeeee...hhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhhh.....eeeeee.hhh................hhhhhhhhhhhhhhh..eeeeeee..hhhhh.hhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ixu C  24 HSVAVIGAPFSQGQKRKGVEHGPAAIREAGLMKRLSSLGCHLKDFGDLSFTPVPKDDLYNNLIVNPRSVGLANQELAEVVSRAVSDGYSCVTLGGDHSLAIGTISGHARHCPDLCVVWVDAHADINTPLTTSSGNLHGQPVSFLLRELQDKVPQLPGFSWIKPCISSASIVYIGLRDVDPPEHFILKNYDIQYFSMRDIDRLGIQKVMERTFDLLIGKRQRPIHLSFDIDAFDPTLAPATGTPVVGGLTYREGMYIAEEIHNTGLLSALDLVEVNPQLATSEEEAKTTANLAVDVIASSFGQTREG 329
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323      

   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  (1, 3)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

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
    38I  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    BEN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    BME  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MN  [ 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 ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:117 - Gly A:118   [ RasMol ]  
    Gly B:117 - Gly B:118   [ RasMol ]  
    Gly C:117 - Gly C:118   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4ixu
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  ARGI2_HUMAN | P78540
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.5.3.1
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  ARGI2_HUMAN | P78540
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ARGI2_HUMAN | P785401pq3 4hze 4i06 4ie2 4ie3 4ixv

(-) Related Entries Specified in the PDB File

1d3v 1pq3 4ixv