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(-) Description

Title :  CRYSTAL STRUCTURE OF SCHISTOSOMA MANSONI ARGINASE IN COMPLEX WITH L-VALINE
 
Authors :  Y. Hai, J. E. Edwards, M. C. Van Zandt, K. F. Hoffmann, D. W. Christianso
Date :  12 Apr 14  (Deposition) - 16 Jul 14  (Release) - 06 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.83
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (3x)
Biol. Unit 2:  B  (3x)
Biol. Unit 3:  C  (3x)
Biol. Unit 4:  D  (3x)
Keywords :  Arginase-Deacetylase Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Hai, J. E. Edwards, M. C. Van Zandt, K. F. Hoffmann, D. W. Christianson
Crystal Structure Of Schistosoma Mansoni Arginase, A Potential Drug Target For The Treatment Of Schistosomiasis.
Biochemistry V. 53 4671 2014
PubMed-ID: 25007099  |  Reference-DOI: 10.1021/BI5004519

(-) Compounds

Molecule 1 - ARGINASE
    Chains: A, B, C, D
    EC Number: 3.5.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SMP_059980
    Organism Common: BLOOD FLUKE
    Organism Scientific: SCHISTOSOMA MANSONI
    Organism Taxid: 6183

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (3x): A   
Biological Unit 2 (3x):  B  
Biological Unit 3 (3x):   C 
Biological Unit 4 (3x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 26)

Asymmetric Unit (4, 26)
No.NameCountTypeFull Name
1GOL7Ligand/IonGLYCEROL
2IMD7Ligand/IonIMIDAZOLE
3MN8Ligand/IonMANGANESE (II) ION
4VAL4Mod. Amino AcidVALINE
Biological Unit 1 (3, 18)
No.NameCountTypeFull Name
1GOL9Ligand/IonGLYCEROL
2IMD6Ligand/IonIMIDAZOLE
3MN-1Ligand/IonMANGANESE (II) ION
4VAL3Mod. Amino AcidVALINE
Biological Unit 2 (3, 18)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2IMD9Ligand/IonIMIDAZOLE
3MN-1Ligand/IonMANGANESE (II) ION
4VAL3Mod. Amino AcidVALINE
Biological Unit 3 (3, 15)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2IMD6Ligand/IonIMIDAZOLE
3MN-1Ligand/IonMANGANESE (II) ION
4VAL3Mod. Amino AcidVALINE
Biological Unit 4 (1, 3)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2IMD-1Ligand/IonIMIDAZOLE
3MN-1Ligand/IonMANGANESE (II) ION
4VAL3Mod. Amino AcidVALINE

(-) Sites  (26, 26)

Asymmetric Unit (26, 26)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:131 , ASP A:154 , ASP A:158 , ASP A:262 , MN A:402 , HOH A:579 , HOH A:581BINDING SITE FOR RESIDUE MN A 401
02AC2SOFTWAREASP A:154 , HIS A:156 , ASP A:262 , ASP A:264 , MN A:401 , HOH A:579BINDING SITE FOR RESIDUE MN A 402
03AC3SOFTWAREASN A:160 , SER A:167 , GLY A:172 , ASP A:213 , HOH A:517 , HOH A:564 , HOH A:565 , HOH A:567 , HOH A:569BINDING SITE FOR RESIDUE VAL A 403
04AC4SOFTWAREASN A:32 , ILE A:38 , GLU A:73 , HOH A:663BINDING SITE FOR RESIDUE GOL A 404
05AC5SOFTWAREASP A:79 , PRO A:80 , GLN A:81 , LYS A:86 , TRP A:87BINDING SITE FOR RESIDUE GOL A 405
06AC6SOFTWAREASP A:65 , CYS A:66 , GLY A:67 , HOH A:705 , GLN C:81 , ARG C:82 , PHE C:83 , GLY C:84 , IMD C:401BINDING SITE FOR RESIDUE GOL A 406
07AC7SOFTWAREILE A:70 , PRO A:71 , GLU A:73 , HOH A:788BINDING SITE FOR RESIDUE IMD A 407
08AC8SOFTWAREGLU A:45BINDING SITE FOR RESIDUE IMD A 408
09AC9SOFTWAREHIS B:131 , ASP B:154 , ASP B:158 , ASP B:262 , MN B:402 , HOH B:535 , HOH B:680BINDING SITE FOR RESIDUE MN B 401
10BC1SOFTWAREASP B:154 , HIS B:156 , ASP B:262 , ASP B:264 , MN B:401 , HOH B:680BINDING SITE FOR RESIDUE MN B 402
11BC2SOFTWAREASP B:158 , ASN B:160 , SER B:167 , GLY B:172 , ASP B:213 , HOH B:531 , HOH B:579 , HOH B:581 , HOH B:590 , HOH B:595BINDING SITE FOR RESIDUE VAL B 403
12BC3SOFTWAREASN B:32 , GLU B:73 , HOH B:629 , HOH B:812BINDING SITE FOR RESIDUE GOL B 404
13BC4SOFTWAREASP B:79 , PRO B:80 , GLN B:81 , LYS B:86 , TRP B:87BINDING SITE FOR RESIDUE GOL B 405
14BC5SOFTWAREPRO B:71 , GLU B:73BINDING SITE FOR RESIDUE IMD B 406
15BC6SOFTWAREGLN B:81 , GLY B:84 , LYS B:86 , ALA B:166 , SER B:167 , HOH B:607BINDING SITE FOR RESIDUE IMD B 407
16BC7SOFTWARETYR B:227 , PHE B:228 , ASP B:232 , HOH B:658 , HOH B:733 , HOH B:790BINDING SITE FOR RESIDUE IMD B 408
17BC8SOFTWAREASP A:68 , ARG A:101 , GOL A:406 , HOH A:550 , HOH A:704 , LEU C:163 , GLN C:351BINDING SITE FOR RESIDUE IMD C 401
18BC9SOFTWAREHIS C:131 , ASP C:154 , ASP C:158 , ASP C:262 , MN C:403 , HOH C:546 , HOH C:547BINDING SITE FOR RESIDUE MN C 402
19CC1SOFTWAREASP C:154 , HIS C:156 , ASP C:262 , ASP C:264 , MN C:402 , HOH C:546BINDING SITE FOR RESIDUE MN C 403
20CC2SOFTWAREASN C:160 , SER C:167 , GLY C:172 , ASP C:213 , HOH C:521 , HOH C:524 , HOH C:549 , HOH C:552 , HOH C:665BINDING SITE FOR RESIDUE VAL C 404
21CC3SOFTWAREASN C:32 , ILE C:38 , GLU C:73 , HOH C:539 , HOH C:728BINDING SITE FOR RESIDUE GOL C 405
22CC4SOFTWAREASP C:79 , PRO C:80 , GLN C:81 , LYS C:86 , TRP C:87BINDING SITE FOR RESIDUE GOL C 406
23CC5SOFTWAREGLN C:81 , GLY C:84 , LYS C:86 , ALA C:166 , SER C:167 , HOH C:669 , HOH C:702BINDING SITE FOR RESIDUE IMD C 407
24CC6SOFTWAREHIS D:131 , ASP D:154 , ASP D:158 , ASP D:262 , MN D:402 , HOH D:510 , HOH D:511BINDING SITE FOR RESIDUE MN D 401
25CC7SOFTWAREASP D:154 , HIS D:156 , ASP D:262 , ASP D:264 , MN D:401 , HOH D:510BINDING SITE FOR RESIDUE MN D 402
26CC8SOFTWAREASN D:160 , SER D:167 , GLY D:172 , ASP D:213 , HOH D:514 , HOH D:515 , HOH D:516 , HOH D:517 , HOH D:563BINDING SITE FOR RESIDUE VAL D 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Q40)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:128 -Gly A:129
2Gly B:128 -Gly B:129
3Gly C:128 -Gly C:129
4Gly D:128 -Gly D:129

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Q40)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q40)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q40)

(-) 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:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee.........hhhhhhhhhhh.hhhhhhhhh..eeeeeee..................hhhhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhh...eeeee.......hhhhh...hhhhh.....hhhhhhhh..hhhhh......hhh.eeeeee...hhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhh......eeeeee.hhh................hhhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhhhhhhhhhh.............hhhhhh..hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q40 A  18 KLLYTSANFLGIPTNRGQPKIGTYQGPELIRKSNFFQLVAEDGIQLTDCGDIIPVELNEAEDPQRFGMKWSRSFSLTTLRIAERVEELMKQSNKSTPLVIVGGDHSMATGTILGHAEAKPDLCVLWIDAHGDINTPLNSASGNMHGMPLSFLVKELQDQIPWLDDFEGIKPCLNASNIAYIGLRDLDAHETHDIRKHGIAYFTMLDVDRMGIEAVIKEALLAVNPRLEKAIHLSFDIDALDPLVAPSTGTAVPGGLTLREGLRICEEVSATGKLSVVELAELNPLLGSQEDVLKTQSSAVHILRACLGHCRSGHLPFKVRNLTDQGIMSRAAHMQ 361
                                    27        37        47        57        67        77        87        97       107  ||   126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356     
                                                                                                                      110|                                                                                                                                                                                                                                                 
                                                                                                                       120                                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee.........hhhhhhhhhhh.hhhhhhhhh..eeeeeee......hhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhh...eeeee.......hhhhh...hhhhh.....hhhhhhhh..hhhhh......hhh.eeeeee...hhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhh......eeeeee.hhh................hhhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhhhhhhhhhhh............hhhhhh..hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q40 B  18 KLLYTSANFLGIPTNRGQPKIGTYQGPELIRKSNFFQLVAEDGIQLTDCGDIIPVELNEAEDPQRFGMKWSRSFSLTTLRIAERVEELMKQSNKSTPLVIVGGDHSMATGTILGHAEAKPDLCVLWIDAHGDINTPLNSASGNMHGMPLSFLVKELQDQIPWLDDFEGIKPCLNASNIAYIGLRDLDAHETHDIRKHGIAYFTMLDVDRMGIEAVIKEALLAVNPRLEKAIHLSFDIDALDPLVAPSTGTAVPGGLTLREGLRICEEVSATGKLSVVELAELNPLLGSQEDVLKTQSSAVHILRACLGHCRSGHLPFKVRNLTDQGIMSRAAHMQ 361
                                    27        37        47        57        67        77        87        97       107  ||   126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356     
                                                                                                                      110|                                                                                                                                                                                                                                                 
                                                                                                                       120                                                                                                                                                                                                                                                 


Chain C from PDB  Type:PROTEIN  Length:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee.........hhhhhhhhhhh.hhhhhhhhh..eeeeeee..................hhhhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhh...eeeee.......hhhhh...hhhhh.....hhhhhhhh..hhhhh......hhh.eeeeee...hhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhh......eeeeee.hhh................hhhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhhhhhhhhhh.............hhhhhh..hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q40 C  18 KLLYTSANFLGIPTNRGQPKIGTYQGPELIRKSNFFQLVAEDGIQLTDCGDIIPVELNEAEDPQRFGMKWSRSFSLTTLRIAERVEELMKQSNKSTPLVIVGGDHSMATGTILGHAEAKPDLCVLWIDAHGDINTPLNSASGNMHGMPLSFLVKELQDQIPWLDDFEGIKPCLNASNIAYIGLRDLDAHETHDIRKHGIAYFTMLDVDRMGIEAVIKEALLAVNPRLEKAIHLSFDIDALDPLVAPSTGTAVPGGLTLREGLRICEEVSATGKLSVVELAELNPLLGSQEDVLKTQSSAVHILRACLGHCRSGHLPFKVRNLTDQGIMSRAAHMQ 361
                                    27        37        47        57        67        77        87        97       107  ||   126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356     
                                                                                                                      110|                                                                                                                                                                                                                                                 
                                                                                                                       120                                                                                                                                                                                                                                                 


Chain D from PDB  Type:PROTEIN  Length:331
                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee.........hhhhhhhhhhhhhhhhhhhhh..eeeeeee......hhhhh.......hhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhh...eeeee.......hhhhh...hhhhh.....hhhhh.....hhhhh......hhh.eeeeee...hhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhh......eeeeee.hhh................hhhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhhhhhhhhhh.....................hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q40 D  18 KLLYTSANFLGIPTNRGQPKIGTYQGPELIRKSNFFQLVAEDGIQLTDCGDIIPVELNEAEDPQRFGMKWSRSFSLTTLRIAERVEELMKQSTPLVIVGGDHSMATGTILGHAEAKPDLCVLWIDAHGDINTPLNSASGNMHGMPLSFLVKELQDQIPWLDDFEGIKPCLNASNIAYIGLRDLDAHETHDIRKHGIAYFTMLDVDRMGIEAVIKEALLAVNPRLEKAIHLSFDIDALDPLVAPSTGTAVPGGLTLREGLRICEEVSATGKLSVVELAELNPLLGSQEDVLKTQSSAVHILRACLGHCRSGHLPFKVRNLTDQGIMSRAAHM 360
                                    27        37        47        57        67        77        87        97       107||     129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359 
                                                                                                                    108|                                                                                                                                                                                                                                               
                                                                                                                     121
   Legend:   → Mismatch (orange background)
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  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 4Q40)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q40)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q40)

(-) Gene Ontology  (6, 6)

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 Related Entries

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

UniProtKB/TrEMBL
        Q6WVP6_SCHMA | Q6WVP6: 4q3p 4q3q 4q3r 4q3s 4q3t 4q3u 4q3v 4q41 4q42

(-) Related Entries Specified in the PDB File

4q3p CRYSTAL STRUCTURE OF SCHISTOSOMA MANSONI ARGINASE
4q3q CRYSTAL STRUCTURE OF SCHISTOSOMA MANSONI ARGINASE IN COMPLEX WITH INHIBITOR ABH
4q3r CRYSTAL STRUCTURE OF SCHISTOSOMA MANSONI ARGINASE IN COMPLEX WITH INHIBITOR ABHDP
4q3s CRYSTAL STRUCTURE OF SCHISTOSOMA MANSONI ARGINASE IN COMPLEX WITH INHIBITOR ABHPE
4q3t CRYSTAL STRUCTURE OF SCHISTOSOMA MANSONI ARGINASE IN COMPLEX WITH INHIBITOR NOHA
4q3u CRYSTAL STRUCTURE OF SCHISTOSOMA MANSONI ARGINASE IN COMPLEX WITH INHIBITOR NOR-NOHA
4q3v CRYSTAL STRUCTURE OF SCHISTOSOMA MANSONI ARGINASE IN COMPLEX WITH INHIBITOR BEC
4q41 CRYSTAL STRUCTURE OF SCHISTOSOMA MANSONI ARGINASE IN COMPLEX WITH L-LYSINE
4q42 CRYSTAL STRUCTURE OF SCHISTOSOMA MANSONI ARGINASE IN COMPLEX WITH L-ORNITHINE