4IXU - JenaLib

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Asym. Unit - sites (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN ARGINASE-2 COMPLEXED WITH INHIBITOR 11D: {(5R)-5-AMINO-5-CARBOXY-5-[(3-ENDO)-8-(3,4-DICHLOROBENZYL)-8-AZABICYCLO[3.2.1]OCT-3-YL]PENTYL}(TRIHYDROXY)BORATE(1-)

Authors :   A. Cousido-Siah, A. Mitschler, F. X. Ruiz, D. Whitehouse, P. Beckett, M Zandt, M. K. Ji, T. Ryder, R. Jagdmann, M. Andreoli, J. Olczak, M. Mazur W. Czestkowski, W. Piotrowska, H. Schroeter, A. Golebiowski, A. Podj

Date :   28 Jan 13 (Deposition) - 11 Dec 13 (Release) - 11 Dec 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)

Keywords :   Metalloenzyme, Alpha/Beta Fold, Hydrolase, Arginine Metabolism, Manganese, Boronate, Mitochondrion, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Golebiowski, D. Whitehouse, R. P. Beckett, M. Van Zandt, M. K. Ji, T. R. Ryder, E. Jagdmann, M. Andreoli, Y. Lee, R. Sheeler, B. Conway, J. Olczak, M. Mazur, W. Czestkowski, W. Piotrowska, A. Cousido-Siah, F. X. Ruiz, A. Mitschler, A. Podjarny, H. Schroeter
Synthesis Of Quaternary Alpha-Amino Acid-Based Arginase Inhibitors Via The Ugi Reaction.
Bioorg. Med. Chem. Lett. V. 23 4837 2013
PubMed-ID: 23886684 | Reference-DOI: 10.1016/J.BMCL.2013.06.092

Molecule 1 - ARGINASE-2, MITOCHONDRIAL
	Chains	:	A, B, C
	EC Number	:	3.5.3.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET23B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	ARG2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	KIDNEY-TYPE ARGINASE, NON-HEPATIC ARGINASE, TYPE II ARGINASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 18)

No.	Name	Count	Type	Full Name
1	38I	3	Ligand/Ion	{(5R)-5-AMINO-5-CARBOXY-5-[(3-ENDO)-8-(3,4-DICHLOROBENZYL)-8-AZABICYCLO[3.2.1]OCT-3-YL]PENTYL}(TRIHYDROXY)BORATE(1-)
2	BEN	3	Ligand/Ion	BENZAMIDINE
3	BME	6	Ligand/Ion	BETA-MERCAPTOETHANOL
4	MN	6	Ligand/Ion	MANGANESE (II) ION

Biological Unit 1 (3, 4)

No.	Name	Count	Type	Full Name
1	38I	1	Ligand/Ion	{(5R)-5-AMINO-5-CARBOXY-5-[(3-ENDO)-8-(3,4-DICHLOROBENZYL)-8-AZABICYCLO[3.2.1]OCT-3-YL]PENTYL}(TRIHYDROXY)BORATE(1-)
2	BEN	1	Ligand/Ion	BENZAMIDINE
3	BME	2	Ligand/Ion	BETA-MERCAPTOETHANOL
4	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	38I	1	Ligand/Ion	{(5R)-5-AMINO-5-CARBOXY-5-[(3-ENDO)-8-(3,4-DICHLOROBENZYL)-8-AZABICYCLO[3.2.1]OCT-3-YL]PENTYL}(TRIHYDROXY)BORATE(1-)
2	BEN	1	Ligand/Ion	BENZAMIDINE
3	BME	2	Ligand/Ion	BETA-MERCAPTOETHANOL
4	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 3 (3, 4)

No.	Name	Count	Type	Full Name
1	38I	1	Ligand/Ion	{(5R)-5-AMINO-5-CARBOXY-5-[(3-ENDO)-8-(3,4-DICHLOROBENZYL)-8-AZABICYCLO[3.2.1]OCT-3-YL]PENTYL}(TRIHYDROXY)BORATE(1-)
2	BEN	1	Ligand/Ion	BENZAMIDINE
3	BME	2	Ligand/Ion	BETA-MERCAPTOETHANOL
4	MN	-1	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:120 , ASP A:143 , ASP A:147 , ASP A:251 , MN A:402 , 38I A:406	BINDING SITE FOR RESIDUE MN A 401
02	AC2	SOFTWARE	ASP A:143 , HIS A:145 , ASP A:251 , ASP A:253 , MN A:401 , 38I A:406	BINDING SITE FOR RESIDUE MN A 402
03	AC3	SOFTWARE	ASN A:83 , ASN A:84 , LEU A:85 , PRO A:151 , LEU A:152 , THR A:153 , THR A:154	BINDING SITE FOR RESIDUE BEN A 403
04	AC4	SOFTWARE	LEU A:58 , PHE A:323	BINDING SITE FOR RESIDUE BME A 404
05	AC5	SOFTWARE	HIS A:133 , CYS A:134 , SER A:290	BINDING SITE FOR RESIDUE BME A 405
06	AC6	SOFTWARE	LEU A:81 , HIS A:120 , ASP A:143 , HIS A:145 , ASP A:147 , ASN A:149 , SER A:156 , HIS A:160 , ASP A:202 , ASP A:251 , ASP A:253 , THR A:265 , GLU A:296 , MN A:401 , MN A:402 , HOH A:503 , HOH A:526 , HOH A:531 , HOH A:544 , HOH A:643 , HOH A:659 , HOH A:671	BINDING SITE FOR RESIDUE 38I A 406
07	AC7	SOFTWARE	HIS B:120 , ASP B:143 , ASP B:147 , ASP B:251 , MN B:402 , 38I B:406	BINDING SITE FOR RESIDUE MN B 401
08	AC8	SOFTWARE	ASP B:143 , HIS B:145 , ASP B:251 , ASP B:253 , MN B:401 , 38I B:406	BINDING SITE FOR RESIDUE MN B 402
09	AC9	SOFTWARE	ASN B:83 , ASN B:84 , LEU B:85 , PRO B:151 , LEU B:152 , THR B:153 , THR B:154	BINDING SITE FOR RESIDUE BEN B 403
10	BC1	SOFTWARE	CYS B:63 , PHE B:323	BINDING SITE FOR RESIDUE BME B 404
11	BC2	SOFTWARE	ASP A:136 , CYS B:134 , HOH B:552 , HOH B:568 , HOH B:767	BINDING SITE FOR RESIDUE BME B 405
12	BC3	SOFTWARE	LEU B:81 , HIS B:120 , ASP B:143 , HIS B:145 , ASP B:147 , ASN B:149 , SER B:155 , SER B:156 , HIS B:160 , ASP B:202 , ASP B:251 , ASP B:253 , THR B:265 , GLU B:296 , MN B:401 , MN B:402 , HOH B:502 , HOH B:505 , HOH B:532 , HOH B:533 , HOH B:548 , HOH B:677 , HOH B:689	BINDING SITE FOR RESIDUE 38I B 406
13	BC4	SOFTWARE	ASP C:143 , HIS C:145 , ASP C:251 , ASP C:253 , MN C:402 , 38I C:406	BINDING SITE FOR RESIDUE MN C 401
14	BC5	SOFTWARE	HIS C:120 , ASP C:143 , ASP C:147 , ASP C:251 , MN C:401 , 38I C:406	BINDING SITE FOR RESIDUE MN C 402
15	BC6	SOFTWARE	ASN C:83 , ASN C:84 , LEU C:85 , PRO C:151 , LEU C:152 , THR C:153 , THR C:154	BINDING SITE FOR RESIDUE BEN C 403
16	BC7	SOFTWARE	HIS C:24 , VAL C:26 , LEU C:58 , CYS C:63 , PHE C:323	BINDING SITE FOR RESIDUE BME C 404
17	BC8	SOFTWARE	VAL C:107 , HIS C:130 , HIS C:133 , PRO C:135	BINDING SITE FOR RESIDUE BME C 405
18	BC9	SOFTWARE	LEU C:81 , HIS C:120 , ASP C:143 , HIS C:145 , ASP C:147 , ASN C:149 , SER C:156 , HIS C:160 , ASP C:202 , ASP C:251 , ASP C:253 , THR C:265 , GLU C:296 , MN C:401 , MN C:402 , HOH C:501 , HOH C:513 , HOH C:522 , HOH C:539 , HOH C:602 , HOH C:633 , HOH C:634	BINDING SITE FOR RESIDUE 38I C 406

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

Asymmetric Unit

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

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

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

(no "Exon" information available for 4IXU)

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

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

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

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Arginase/deacetylase (138)

Superfamily: Arginase/deacetylase (138)

Family: Arginase-like amidino hydrolases (97)

Protein domain: Arginase (73)

Human (Homo sapiens), isoform II, mitochondrial [TaxId: 9606] (7)

1a	d4ixua_	A:
1b	d4ixub_	B:
1c	d4ixuc_	C:

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Gly A:117 - Gly A:118	[ RasMol ]
		Gly B:117 - Gly B:118	[ RasMol ]
		Gly C:117 - Gly C:118	[ RasMol ]

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	ARGI2_HUMAN \| P78540	:	1pq3 4hze 4i06 4ie2 4ie3 4ixv

Description

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Chains, Units

Ligands, Modified Residues, Ions (4, 18)

Sites (18, 18)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

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