4Q3V - JenaLib

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Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

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

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 :   2.70

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, 17)

No.	Name	Count	Type	Full Name
1	GOL	6	Ligand/Ion	GLYCEROL
2	MN	8	Ligand/Ion	MANGANESE (II) ION
3	S2C	3	Ligand/Ion	S-2-(BORONOETHYL)-L-CYSTEINE

Biological Unit 1 (2, 9)

No.	Name	Count	Type	Full Name
1	GOL	6	Ligand/Ion	GLYCEROL
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	S2C	3	Ligand/Ion	S-2-(BORONOETHYL)-L-CYSTEINE

Biological Unit 2 (2, 9)

No.	Name	Count	Type	Full Name
1	GOL	6	Ligand/Ion	GLYCEROL
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	S2C	3	Ligand/Ion	S-2-(BORONOETHYL)-L-CYSTEINE

Biological Unit 3 (2, 9)

No.	Name	Count	Type	Full Name
1	GOL	6	Ligand/Ion	GLYCEROL
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	S2C	3	Ligand/Ion	S-2-(BORONOETHYL)-L-CYSTEINE

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	S2C	-1	Ligand/Ion	S-2-(BORONOETHYL)-L-CYSTEINE

Asymmetric Unit (17, 17)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:131 , ASP A:154 , ASP A:158 , ASP A:262 , MN A:402 , S2C 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 , S2C A:405	BINDING SITE FOR RESIDUE MN A 402
03	AC3	SOFTWARE	ASP A:79 , 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:540	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 , ASP A:213 , ASP A:262 , ASP A:264 , THR A:276 , GLU A:307 , MN A:401 , MN A:402 , HOH A:538 , HOH A:609 , HOH A:624	BINDING SITE FOR RESIDUE S2C A 405
06	AC6	SOFTWARE	HIS B:131 , ASP B:154 , ASP B:158 , ASP B:262 , MN B:402 , S2C 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 , S2C B:405	BINDING SITE FOR RESIDUE MN B 402
08	AC8	SOFTWARE	ASP B:79 , LYS B:86 , TRP B:87	BINDING SITE FOR RESIDUE GOL B 403
09	AC9	SOFTWARE	ASN B:32 , TYR B:41 , GLU B:73 , HOH B:609	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 , ASP B:213 , ASP B:262 , ASP B:264 , THR B:276 , GLU B:307 , MN B:401 , MN B:402 , HOH B:528 , HOH B:532	BINDING SITE FOR RESIDUE S2C B 405
11	BC2	SOFTWARE	ASP C:154 , HIS C:156 , ASP C:262 , ASP C:264 , MN C:402 , S2C C:405	BINDING SITE FOR RESIDUE MN C 401
12	BC3	SOFTWARE	HIS C:131 , ASP C:154 , ASP C:158 , ASP C:262 , MN C:401 , S2C C:405	BINDING SITE FOR RESIDUE MN C 402
13	BC4	SOFTWARE	GLU C:76 , 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:565	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 , ASP C:213 , ASP C:262 , ASP C:264 , THR C:276 , GLU C:307 , MN C:401 , MN C:402 , HOH C:535	BINDING SITE FOR RESIDUE S2C C 405
16	BC7	SOFTWARE	HIS D:131 , ASP D:154 , ASP D:158 , ASP D:262 , MN D:401 , HOH D:502	BINDING SITE FOR RESIDUE MN D 400
17	BC8	SOFTWARE	ASP D:154 , HIS D:156 , ASP D:262 , ASP D:264 , MN D:400 , HOH D:502	BINDING SITE FOR RESIDUE MN D 401

(no "SS Bond" information available for 4Q3V)

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 4Q3V)

(no "PROSITE Motif" information available for 4Q3V)

(no "Exon" information available for 4Q3V)

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:337
                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee.........hhhhhhhhhhhhhhhhhhhhh..eeeeeee..................hhhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhh...eeeee.......hhhhh...hhhhh.....hhhhh.....hhhhh......hhh.eeeeee...hhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhh......eeeeee.hhh................hhhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhhhhhhhhhh.....................hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q3v A  17 PKLLYTSANFLGIPTNRGQPKIGTYQGPELIRKSNFFQLVAEDGIQLTDCGDIIPVELNEAEDPQRFGMKWSRSFSLTTLRIAERVEELMKQSNKSTPLVIVGGDHSMATGTILGHAEAKPDLCVLWIDAHGDINTPLNSASGNMHGMPLSFLVKELQDQIPWLDDFEGIKPCLNASNIAYIGLRDLDAHETHDIRKHGIAYFTMLDVDRMGIEAVIKEALLAVNPRLEKAIHLSFDIDALDPLVAPSTGTAVPGGLTLREGLRICEEVSATGKLSVVELAELNPLLGSQEDVLKTQSSAVHILRACLGHCRSGHLPFKVRNLTDQGIMSRAAHMQT 362
                                    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:338
                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee.........hhhhhhhhhhh.hhhhhhhhh..eeeeeee..................hhhhhhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhhh...eeeee.......hhhhh...hhhhh.....hhhhhhhh..hhhhh......hhh.eeeeee...hhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhh......eeeeee.hhh................hhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhhhhhhhh..............hhhhh..hhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q3v B  17 PKLLYTSANFLGIPTNRGQPKIGTYQGPELIRKSNFFQLVAEDGIQLTDCGDIIPVELNEAEDPQRFGMKWSRSFSLTTLRIAERVEELMKQSNKKSTPLVIVGGDHSMATGTILGHAEAKPDLCVLWIDAHGDINTPLNSASGNMHGMPLSFLVKELQDQIPWLDDFEGIKPCLNASNIAYIGLRDLDAHETHDIRKHGIAYFTMLDVDRMGIEAVIKEALLAVNPRLEKAIHLSFDIDALDPLVAPSTGTAVPGGLTLREGLRICEEVSATGKLSVVELAELNPLLGSQEDVLKTQSSAVHILRACLGHCRSGHLPFKVRNLTDQGIMSRAAHMQT 362
                                    26        36        46        56        66        76        86        96       106    || 124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354        
                                                                                                                        111|                                                                                                                                                                                                                                                  
                                                                                                                         120

Chain C from PDB  Type:PROTEIN  Length:339
                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeee.........hhhhhhhhhhh.hhhhhhhh...eeeeeee..................hhhhhhhhhhhhhhhhhhhhhhh......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
                 4q3v C  16 KPKLLYTSANFLGIPTNRGQPKIGTYQGPELIRKSNFFQLVAEDGIQLTDCGDIIPVELNEAEDPQRFGMKWSRSFSLTTLRIAERVEELMKQSNKKSTPLVIVGGDHSMATGTILGHAEAKPDLCVLWIDAHGDINTPLNSASGNMHGMPLSFLVKELQDQIPWLDDFEGIKPCLNASNIAYIGLRDLDAHETHDIRKHGIAYFTMLDVDRMGIEAVIKEALLAVNPRLEKAIHLSFDIDALDPLVAPSTGTAVPGGLTLREGLRICEEVSATGKLSVVELAELNPLLGSQEDVLKTQSSAVHILRACLGHCRSGHLPFKVRNLTDQGIMSRAAHMQT 362
                                    25        35        45        55        65        75        85        95       105     ||123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353         
                                                                                                                         111|                                                                                                                                                                                                                                                  
                                                                                                                          120

Chain D from PDB  Type:PROTEIN  Length:329
                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.........hhhhhhhhhhh.hhhhhhhh...eeeeeee..................hhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhh...eeeee...............hhhhh.....hhhhh.....hhhhh......hhh.eeeeee...hhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhh......eeeeee.hhh................hhhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhhhhhhhhhh.....................hhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q3v D  19 LLYTSANFLGIPTNRGQPKIGTYQGPELIRKSNFFQLVAEDGIQLTDCGDIIPVELNEAEDPQRFGMKWSRSFSLTTLRIAERVEELMKSTPLVIVGGDHSMATGTILGHAEAKPDLCVLWIDAHGDINTPLNSASGNMHGMPLSFLVKELQDQIPWLDDFEGIKPCLNASNIAYIGLRDLDAHETHDIRKHGIAYFTMLDVDRMGIEAVIKEALLAVNPRLEKAIHLSFDIDALDPLVAPSTGTAVPGGLTLREGLRICEEVSATGKLSVVELAELNPLLGSQEDVLKTQSSAVHILRACLGHCRSGHLPFKVRNLTDQGIMSRAAHM 360
                                    28        38        48        58        68        78        88        98       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351         
                                                                                                                  107|                                                                                                                                                                                                                                               
                                                                                                                   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 4Q3V)

(no "CATH Domain" information available for 4Q3V)

(no "Pfam Domain" information available for 4Q3V)

Asymmetric Unit(hide GO term definitions)

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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	4q3v
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	3.5.3.1
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UniProtKB/TrEMBL
	Q6WVP6_SCHMA \| Q6WVP6	:	4q3p 4q3q 4q3r 4q3s 4q3t 4q3u 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
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
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

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 17)

Sites (17, 17)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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Exons (0, 0)

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