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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ARGINASE-2 COMPLEXED WITH INHIBITOR 2D: {(5R)-5-AMINO-5-CARBOXY-5-[1-(4-CHLOROBENZYL)PIPERIDIN-4-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 :  2.30
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Biol. Unit 4:  C  (1x)
Keywords :  Metalloenzyme, Alpha/Beta Fold, Hydrolase, Arginine Metabolism, 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
    FragmentUNP RESIDUES 24-329
    GeneARG2
    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)ABC
Biological Unit 2 (1x)A  
Biological Unit 3 (1x) B 
Biological Unit 4 (1x)  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 15)

Asymmetric Unit (4, 15)
No.NameCountTypeFull Name
1BEN3Ligand/IonBENZAMIDINE
2BME3Ligand/IonBETA-MERCAPTOETHANOL
3MN6Ligand/IonMANGANESE (II) ION
4XA13Ligand/Ion{(5R)-5-AMINO-5-CARBOXY-5-[1-(4-CHLOROBENZYL)PIPERIDIN-4-YL]PENTYL}(TRIHYDROXY)BORATE(1-)
Biological Unit 1 (3, 9)
No.NameCountTypeFull Name
1BEN3Ligand/IonBENZAMIDINE
2BME3Ligand/IonBETA-MERCAPTOETHANOL
3MN-1Ligand/IonMANGANESE (II) ION
4XA13Ligand/Ion{(5R)-5-AMINO-5-CARBOXY-5-[1-(4-CHLOROBENZYL)PIPERIDIN-4-YL]PENTYL}(TRIHYDROXY)BORATE(1-)
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1BEN1Ligand/IonBENZAMIDINE
2BME1Ligand/IonBETA-MERCAPTOETHANOL
3MN-1Ligand/IonMANGANESE (II) ION
4XA11Ligand/Ion{(5R)-5-AMINO-5-CARBOXY-5-[1-(4-CHLOROBENZYL)PIPERIDIN-4-YL]PENTYL}(TRIHYDROXY)BORATE(1-)
Biological Unit 3 (3, 3)
No.NameCountTypeFull Name
1BEN1Ligand/IonBENZAMIDINE
2BME1Ligand/IonBETA-MERCAPTOETHANOL
3MN-1Ligand/IonMANGANESE (II) ION
4XA11Ligand/Ion{(5R)-5-AMINO-5-CARBOXY-5-[1-(4-CHLOROBENZYL)PIPERIDIN-4-YL]PENTYL}(TRIHYDROXY)BORATE(1-)
Biological Unit 4 (3, 3)
No.NameCountTypeFull Name
1BEN1Ligand/IonBENZAMIDINE
2BME1Ligand/IonBETA-MERCAPTOETHANOL
3MN-1Ligand/IonMANGANESE (II) ION
4XA11Ligand/Ion{(5R)-5-AMINO-5-CARBOXY-5-[1-(4-CHLOROBENZYL)PIPERIDIN-4-YL]PENTYL}(TRIHYDROXY)BORATE(1-)

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:120 , ASP A:143 , ASP A:147 , ASP A:251 , MN A:402 , XA1 A:405BINDING SITE FOR RESIDUE MN A 401
02AC2SOFTWAREASP A:143 , HIS A:145 , ASP A:251 , ASP A:253 , MN A:401 , XA1 A:405BINDING 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:61 , CYS A:63 , HIS A:284 , PHE A:323BINDING SITE FOR RESIDUE BME A 404
05AC5SOFTWARELYS A:38 , HIS A:120 , ASP A:143 , HIS A:145 , ASP A:147 , ASN A:149 , SER A:155 , 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:516 , HOH A:558 , HOH A:559 , HOH A:573 , HOH A:574 , HOH A:599BINDING SITE FOR RESIDUE XA1 A 405
06AC6SOFTWAREHIS B:120 , ASP B:143 , ASP B:147 , ASP B:251 , MN B:402 , XA1 B:405BINDING SITE FOR RESIDUE MN B 401
07AC7SOFTWAREASP B:143 , HIS B:145 , ASP B:251 , ASP B:253 , MN B:401 , XA1 B:405BINDING SITE FOR RESIDUE MN B 402
08AC8SOFTWAREASN 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
09AC9SOFTWARELEU B:61 , CYS B:63 , PHE B:323BINDING SITE FOR RESIDUE BME B 404
10BC1SOFTWAREHIS B:120 , ASP B:143 , HIS B:145 , ASP B:147 , ASN B:149 , 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:515 , HOH B:524 , HOH B:536 , HOH B:544 , HOH B:556 , HOH B:639BINDING SITE FOR RESIDUE XA1 B 405
11BC2SOFTWAREASP C:143 , HIS C:145 , ASP C:251 , ASP C:253 , MN C:402 , XA1 C:405BINDING SITE FOR RESIDUE MN C 401
12BC3SOFTWAREHIS C:120 , ASP C:143 , ASP C:147 , ASP C:251 , MN C:401 , XA1 C:405BINDING SITE FOR RESIDUE MN C 402
13BC4SOFTWAREASN 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
14BC5SOFTWAREHIS C:24 , LEU C:61 , CYS C:63 , PHE C:323BINDING SITE FOR RESIDUE BME C 404
15BC6SOFTWAREHIS C:120 , ASP C:143 , HIS C:145 , ASP C:147 , ASN C:149 , SER C:155 , 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:519 , HOH C:522 , HOH C:527 , HOH C:529 , HOH C:530 , HOH C:544 , HOH C:559BINDING SITE FOR RESIDUE XA1 C 405

(-) SS Bonds  (0, 0)

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

(-) 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 4IXV)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IXV)

(-) 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 d4ixva_ A: 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
                 4ixv 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 d4ixvb_ B: Arginase                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee..........hhhhhhhhhhhhhhhhhhhhh..eeeeeee.................hhhhhhhhhhhhhhhhhhhhhh.eeeeee..hhhhhhhhhhhhhhhh...eeeee...............hhhhhhhhhhhhhhhhhh.............hhh.eeeeee...hhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhhh.....eeeeee.hhh................hhhhhhhhhhhhhhh..eeeeeee..hhhhh.hhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ixv 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 d4ixvc_ C: Arginase                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee..........hhhhhhhhhhhhhhhhhhhhh..eeeeeee.................hhhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh...eeeee...............hhhhhhhhhhhhhhhhhh.............hhh.eeeeee...hhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhhh.....eeeeee.hhh................hhhhhhhhhhhhhhh..eeeeeee..hhhhh.hhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ixv 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 4IXV)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

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        ARGI2_HUMAN | P785401pq3 4hze 4i06 4ie2 4ie3 4ixu

(-) Related Entries Specified in the PDB File

1d3v 1pq3 4ixu