4Q3T - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF SCHISTOSOMA MANSONI ARGINASE IN COMPLEX WITH INHIBITOR NOHA

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 :   2.14

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-Hydrolase Inhibitor Complex (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

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

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
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)

Asymmetric Unit (3, 18)

No.	Name	Count	Type	Full Name
1	GOL	6	Ligand/Ion	GLYCEROL
2	HAR	4	Ligand/Ion	N-OMEGA-HYDROXY-L-ARGININE
3	MN	8	Ligand/Ion	MANGANESE (II) ION

Biological Unit 1 (2, 9)

No.	Name	Count	Type	Full Name
1	GOL	6	Ligand/Ion	GLYCEROL
2	HAR	3	Ligand/Ion	N-OMEGA-HYDROXY-L-ARGININE
3	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 2 (2, 9)

No.	Name	Count	Type	Full Name
1	GOL	6	Ligand/Ion	GLYCEROL
2	HAR	3	Ligand/Ion	N-OMEGA-HYDROXY-L-ARGININE
3	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 3 (2, 9)

No.	Name	Count	Type	Full Name
1	GOL	6	Ligand/Ion	GLYCEROL
2	HAR	3	Ligand/Ion	N-OMEGA-HYDROXY-L-ARGININE
3	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 4 (1, 3)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	HAR	3	Ligand/Ion	N-OMEGA-HYDROXY-L-ARGININE
3	MN	-1	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:131 , ASP A:154 , ASP A:158 , ASP A:262 , MN A:402 , HAR A:405	BINDING SITE FOR RESIDUE MN A 401
02	AC2	SOFTWARE	ASP A:154 , HIS A:156 , ASP A:262 , ASP A:264 , MN A:401 , HAR A:405	BINDING SITE FOR RESIDUE MN A 402
03	AC3	SOFTWARE	ASP A:79 , PRO A:80 , GLN A:81 , LYS A:86 , TRP A:87	BINDING SITE FOR RESIDUE GOL A 403
04	AC4	SOFTWARE	ASN A:32 , GLU A:73 , HOH A:571	BINDING SITE FOR RESIDUE GOL A 404
05	AC5	SOFTWARE	HIS A:131 , ASP A:154 , HIS A:156 , ASP A:158 , ASN A:160 , SER A:167 , HIS A:171 , GLY A:172 , ASP A:213 , ASP A:262 , ASP A:264 , THR A:276 , GLU A:307 , MN A:401 , MN A:402 , HOH A:580 , HOH A:581 , HOH A:584 , HOH A:588 , HOH A:660 , HOH A:668	BINDING SITE FOR RESIDUE HAR A 405
06	AC6	SOFTWARE	HIS B:131 , ASP B:154 , ASP B:158 , ASP B:262 , MN B:402 , HAR B:405	BINDING SITE FOR RESIDUE MN B 401
07	AC7	SOFTWARE	ASP B:154 , HIS B:156 , ASP B:262 , ASP B:264 , MN B:401 , HAR B:405	BINDING SITE FOR RESIDUE MN B 402
08	AC8	SOFTWARE	GLU B:76 , ASP B:79 , PRO B:80 , GLN B:81 , LYS B:86 , TRP B:87	BINDING SITE FOR RESIDUE GOL B 403
09	AC9	SOFTWARE	ASN B:32 , GLU B:73 , HOH B:659	BINDING SITE FOR RESIDUE GOL B 404
10	BC1	SOFTWARE	HIS B:131 , ASP B:154 , HIS B:156 , ASP B:158 , ASN B:160 , SER B:167 , HIS B:171 , GLY B:172 , ASP B:213 , ASP B:262 , ASP B:264 , THR B:276 , GLU B:307 , MN B:401 , MN B:402 , HOH B:596 , HOH B:618 , HOH B:689 , HOH B:690	BINDING SITE FOR RESIDUE HAR B 405
11	BC2	SOFTWARE	HIS C:131 , ASP C:154 , ASP C:158 , ASP C:262 , MN C:402 , HAR C:405	BINDING SITE FOR RESIDUE MN C 401
12	BC3	SOFTWARE	ASP C:154 , HIS C:156 , ASP C:262 , ASP C:264 , MN C:401 , HAR C:405	BINDING SITE FOR RESIDUE MN C 402
13	BC4	SOFTWARE	ASP C:79 , PRO C:80 , GLN C:81 , LYS C:86 , TRP C:87	BINDING SITE FOR RESIDUE GOL C 403
14	BC5	SOFTWARE	ASN C:32 , ILE C:38 , GLU C:73 , HOH C:634	BINDING SITE FOR RESIDUE GOL C 404
15	BC6	SOFTWARE	HIS C:131 , ASP C:154 , HIS C:156 , ASP C:158 , ASN C:160 , SER C:167 , HIS C:171 , GLY C:172 , ASP C:213 , ASP C:262 , ASP C:264 , THR C:276 , GLU C:307 , MN C:401 , MN C:402 , HOH C:559 , HOH C:605 , HOH C:606	BINDING SITE FOR RESIDUE HAR C 405
16	BC7	SOFTWARE	ASP D:154 , HIS D:156 , ASP D:158 , ASN D:160 , SER D:167 , HIS D:171 , GLY D:172 , ASP D:262 , GLU D:307 , MN D:402 , MN D:403 , HOH D:515 , HOH D:517	BINDING SITE FOR RESIDUE HAR D 401
17	BC8	SOFTWARE	HIS D:131 , ASP D:154 , ASP D:158 , ASP D:262 , HAR D:401 , MN D:403	BINDING SITE FOR RESIDUE MN D 402
18	BC9	SOFTWARE	ASP D:154 , HIS D:156 , ASP D:262 , ASP D:264 , HAR D:401 , MN D:402	BINDING SITE FOR RESIDUE MN D 403

(no "SS Bond" information available for 4Q3T)

Asymmetric Unit

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

(no "SAP(SNP)/Variant" information available for 4Q3T)

(no "PROSITE Motif" information available for 4Q3T)

(no "Exon" information available for 4Q3T)

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:336
                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeee.........hhhhhhhhhhh.hhhhhhhhh..eeeeeee..................hhhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhh...eeeee...............hhhhh.....hhhhhhhh..hhhhh......hhh.eeeeee...hhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhh......eeeeee.hhh................hhhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhhhhhhhhhh.............hhhhhh..hhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4q3t A  17 PKLLYTSANFLGIPTNRGQPKIGTYQGPELIRKSNFFQLVAEDGIQLTDCGDIIPVELNEAEDPQRFGMKWSRSFSLTTLRIAERVEELMKQSNKSTPLVIVGGDHSMATGTILGHAEAKPDLCVLWIDAHGDINTPLNSASGNMHGMPLSFLVKELQDQIPWLDDFEGIKPCLNASNIAYIGLRDLDAHETHDIRKHGIAYFTMLDVDRMGIEAVIKEALLAVNPRLEKAIHLSFDIDALDPLVAPSTGTAVPGGLTLREGLRICEEVSATGKLSVVELAELNPLLGSQEDVLKTQSSAVHILRACLGHCRSGHLPFKVRNLTDQGIMSRAAHMQ 361
                                    26        36        46        56        66        76        86        96       106   ||  125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355      
                                                                                                                       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.......hhhhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhh...eeeee...............hhhhh.....hhhhh.....hhhhh......hhh.eeeeee...hhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhh......eeeeee.hhh................hhhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhhhhhhhhhhh....................hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q3t B  17 PKLLYTSANFLGIPTNRGQPKIGTYQGPELIRKSNFFQLVAEDGIQLTDCGDIIPVELNEAEDPQRFGMKWSRSFSLTTLRIAERVEELMKQSSTPLVIVGGDHSMATGTILGHAEAKPDLCVLWIDAHGDINTPLNSASGNMHGMPLSFLVKELQDQIPWLDDFEGIKPCLNASNIAYIGLRDLDAHETHDIRKHGIAYFTMLDVDRMGIEAVIKEALLAVNPRLEKAIHLSFDIDALDPLVAPSTGTAVPGGLTLREGLRICEEVSATGKLSVVELAELNPLLGSQEDVLKTQSSAVHILRACLGHCRSGHLPFKVRNLTDQGIMSRAAHMQT 362
                                    26        36        46        56        66        76        86        96       106  ||   127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357     
                                                                                                                      109|                                                                                                                                                                                                                                                 
                                                                                                                       121

Chain C from PDB  Type:PROTEIN  Length:334
                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee.........hhhhhhhhhhh.hhhhhhhhh..eeeeeee..................hhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhh...eeeee.......hhhhh...hhhhh.....hhhhhhhh..hhhhh......hhh.eeeeee...hhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhh......eeeeee.hhh................hhhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhhhhhhhhhh.............hhhhhh..hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q3t C  17 PKLLYTSANFLGIPTNRGQPKIGTYQGPELIRKSNFFQLVAEDGIQLTDCGDIIPVELNEAEDPQRFGMKWSRSFSLTTLRIAERVEELMKQSTPLVIVGGDHSMATGTILGHAEAKPDLCVLWIDAHGDINTPLNSASGNMHGMPLSFLVKELQDQIPWLDDFEGIKPCLNASNIAYIGLRDLDAHETHDIRKHGIAYFTMLDVDRMGIEAVIKEALLAVNPRLEKAIHLSFDIDALDPLVAPSTGTAVPGGLTLREGLRICEEVSATGKLSVVELAELNPLLGSQEDVLKTQSSAVHILRACLGHCRSGHLPFKVRNLTDQGIMSRAAHMQT 362
                                    26        36        46        56        66        76        86        96       106 ||    128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358    
                                                                                                                     108|                                                                                                                                                                                                                                                 
                                                                                                                      121

Chain D from PDB  Type:PROTEIN  Length:329
                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.........hhhhhhhhhhhhhhhhhhhh...eeeeeee..................hhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhh...eeeee...............hhhhh.....hhhhhhhh.............hhh.eeeeee...hhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhh......eeeeee.hhh................hhhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhhhhhhhhhhh............hhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q3t D  19 LLYTSANFLGIPTNRGQPKIGTYQGPELIRKSNFFQLVAEDGIQLTDCGDIIPVELNEAEDPQRFGMKWSRSFSLTTLRIAERVEELMKQSTPLVIVGGDHSMATGTILGHAEAKPDLCVLWIDAHGDINTPLNSASGNMHGMPLSFLVKELQDQIPWLDDFEGIKPCLNASNIAYIGLRDLDAHETHDIRKHGIAYFTMLDVDRMGIEAVIKEALLAVNPRLEKAIHLSFDIDALDPLVAPSTGTAVPGGLTLREGLRICEEVSATGKLSVVELAELNPLLGSQEDVLKTQSSAVHILRACLGHCRSGHLPFKVRNLTDQGIMSRAAH 359
                                    28        38        48        58        68        78        88        98       108|      130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350         
                                                                                                                   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 '\|'

(no "SCOP Domain" information available for 4Q3T)

(no "CATH Domain" information available for 4Q3T)

(no "Pfam Domain" information available for 4Q3T)

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Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:128 - Gly A:129	[ RasMol ]
		Gly B:128 - Gly B:129	[ RasMol ]
		Gly C:128 - Gly C:129	[ RasMol ]
		Gly D:128 - Gly D:129	[ RasMol ]

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	Q6WVP6_SCHMA \| Q6WVP6	:	4q3p 4q3q 4q3r 4q3s 4q3u 4q3v 4q40 4q41 4q42

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
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
4q40	CRYSTAL STRUCTURE OF SCHISTOSOMA MANSONI ARGINASE IN COMPLEX WITH L-VALINE
4q41	CRYSTAL STRUCTURE OF SCHISTOSOMA MANSONI ARGINASE IN COMPLEX WITH L-LYSINE
4q42	CRYSTAL STRUCTURE OF SCHISTOSOMA MANSONI ARGINASE IN COMPLEX WITH L-ORNITHINE

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (3, 18)

Sites (18, 18)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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