4IE3 - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN ARGINASE-2 COMPLEXED WITH INHBITOR 1O

Authors :   A. Cousido-Siah, A. Mitschler, F. X. Ruiz, P. Beckett, M. C. Van Zandt, D. Whitehouse, T. Ryder, E. Jagdmann, M. Andreoli, A. Mazur, M. Padman H. Schroeter, A. Golebiowski, A. Podjarny

Date :   13 Dec 12 (Deposition) - 20 Mar 13 (Release) - 03 Apr 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.35

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A,B,C  (1x)
Biol. Unit 2: A  (1x)
Biol. Unit 3: B  (1x)
Biol. Unit 4: C  (1x)

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

Reference :   A. Golebiowski, R. Paul Beckett, M. Van Zandt, M. K. Ji, D. Whitehouse, T. R. Ryder, E. Jagdmann, M. Andreoli, A. Mazur, M. Padmanilayam, A. Cousido-Siah, A. Mitschler, F. X. Ruiz, A. Podjarny, H. Schroeter
2-Substituted-2-Amino-6-Boronohexanoic Acids As Arginase Inhibitors.
Bioorg. Med. Chem. Lett. V. 23 2027 2013
PubMed-ID: 23453840 | Reference-DOI: 10.1016/J.BMCL.2013.02.024

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	B	C
Biological Unit 2 (1x)	:	A
Biological Unit 3 (1x)	:		B
Biological Unit 4 (1x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 16)

No.	Name	Count	Type	Full Name
1	1EE	3	Ligand/Ion	[(5R)-5-AMINO-5-CARBOXY-7-(4-HYDROXYPIPERIDIN-1-YL)HEPTYL](TRIHYDROXY)BORATE(1-)
2	BEN	3	Ligand/Ion	BENZAMIDINE
3	BME	4	Ligand/Ion	BETA-MERCAPTOETHANOL
4	MN	6	Ligand/Ion	MANGANESE (II) ION

Biological Unit 1 (3, 10)

No.	Name	Count	Type	Full Name
1	1EE	3	Ligand/Ion	[(5R)-5-AMINO-5-CARBOXY-7-(4-HYDROXYPIPERIDIN-1-YL)HEPTYL](TRIHYDROXY)BORATE(1-)
2	BEN	3	Ligand/Ion	BENZAMIDINE
3	BME	4	Ligand/Ion	BETA-MERCAPTOETHANOL
4	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	1EE	1	Ligand/Ion	[(5R)-5-AMINO-5-CARBOXY-7-(4-HYDROXYPIPERIDIN-1-YL)HEPTYL](TRIHYDROXY)BORATE(1-)
2	BEN	1	Ligand/Ion	BENZAMIDINE
3	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
4	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 3 (3, 4)

No.	Name	Count	Type	Full Name
1	1EE	1	Ligand/Ion	[(5R)-5-AMINO-5-CARBOXY-7-(4-HYDROXYPIPERIDIN-1-YL)HEPTYL](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 4 (3, 3)

No.	Name	Count	Type	Full Name
1	1EE	1	Ligand/Ion	[(5R)-5-AMINO-5-CARBOXY-7-(4-HYDROXYPIPERIDIN-1-YL)HEPTYL](TRIHYDROXY)BORATE(1-)
2	BEN	1	Ligand/Ion	BENZAMIDINE
3	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
4	MN	-1	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:120 , ASP A:143 , ASP A:147 , ASP A:251 , MN A:402 , 1EE A:405	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 , 1EE A:405	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	HIS A:24 , CYS A:63 , HIS A:284 , PHE A:323	BINDING SITE FOR RESIDUE BME A 404
05	AC5	SOFTWARE	HIS A:120 , ASP A:143 , HIS A:145 , ASP A:147 , ASN A:149 , SER A:155 , SER A:156 , HIS A:160 , ASP A:202 , GLU A:205 , ASP A:251 , ASP A:253 , THR A:265 , GLU A:296 , MN A:401 , MN A:402 , HOH A:503 , HOH A:515 , HOH A:520 , HOH A:532 , HOH A:536 , HOH A:550 , HOH A:565	BINDING SITE FOR RESIDUE 1EE A 405
06	AC6	SOFTWARE	HIS B:120 , ASP B:143 , ASP B:147 , ASP B:251 , MN B:402 , 1EE B:406	BINDING SITE FOR RESIDUE MN B 401
07	AC7	SOFTWARE	ASP B:143 , HIS B:145 , ASP B:251 , ASP B:253 , MN B:401 , 1EE B:406	BINDING SITE FOR RESIDUE MN B 402
08	AC8	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
09	AC9	SOFTWARE	HIS B:24 , LEU B:61 , CYS B:63 , PHE B:323	BINDING SITE FOR RESIDUE BME B 404
10	BC1	SOFTWARE	PRO A:135 , CYS B:134 , PRO B:135 , ASP B:136 , PRO B:245 , HOH B:532 , HOH B:721	BINDING SITE FOR RESIDUE BME B 405
11	BC2	SOFTWARE	HIS B:120 , ASP B:143 , HIS B:145 , ASP B:147 , ASN B:149 , SER B:156 , HIS B:160 , GLY B:161 , ASP B:202 , ASP B:251 , ASP B:253 , THR B:265 , GLU B:296 , MN B:401 , MN B:402 , HOH B:506 , HOH B:509 , HOH B:522 , HOH B:548 , HOH B:567 , HOH B:595	BINDING SITE FOR RESIDUE 1EE B 406
12	BC3	SOFTWARE	ASP C:143 , HIS C:145 , ASP C:251 , ASP C:253 , MN C:402 , 1EE C:405	BINDING SITE FOR RESIDUE MN C 401
13	BC4	SOFTWARE	HIS C:120 , ASP C:143 , ASP C:147 , ASP C:251 , MN C:401 , 1EE C:405	BINDING SITE FOR RESIDUE MN C 402
14	BC5	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
15	BC6	SOFTWARE	HIS C:24 , LEU C:61 , CYS C:63 , PHE C:323	BINDING SITE FOR RESIDUE BME C 404
16	BC7	SOFTWARE	HIS C:120 , ASP C:143 , HIS C:145 , ASP C:147 , ASN C:149 , SER C:155 , SER C:156 , HIS C:160 , ASP C:202 , ASP C:251 , ASP C:253 , THR C:265 , GLU C:296 , MN C:401 , MN C:402 , HOH C:505 , HOH C:506 , HOH C:515 , HOH C:516 , HOH C:529 , HOH C:551 , HOH C:608	BINDING SITE FOR RESIDUE 1EE C 405

(no "SS Bond" information available for 4IE3)

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 4IE3)

(no "PROSITE Motif" information available for 4IE3)

(no "Exon" information available for 4IE3)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4ie3a_ A: Arginase                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee.........hhhhhhhhhhhhhhhhhhhhh..eeeeeee.................hhhhhhhhhhhhhhhhhhhhhh.eeeeeee.hhhhhhhhhhhhhhhh...eeeee...............hhhhhhhhhhhhhhhhhh.............hhh.eeeeee...hhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhhh.....eeeeee.hhh................hhhhhhhhhhhhhhh..eeeeeee..hhhhh.hhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ie3 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 d4ie3b_ B: Arginase                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee..........hhhhhhhhhhhhhhhhhhhhh..eeeeeee.................hhhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh...eeeee...............hhhhhhhhhhhhhhh................hhh.eeeeee...hhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhhh.....eeeeee.hhh................hhhhhhhhhhhhhhhh.eeeeeee..hhhhh.hhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ie3 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 d4ie3c_ C: Arginase                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee..........hhhhhhhhhhhhhhhhhhhhh..eeeeeee.................hhhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh...eeeee...............hhhhhhhhhhhhhhhhhh.............hhh.eeeeee...hhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhhh.....eeeeee.hhh................hhhhhhhhhhhhhhh..eeeeeee..hhhhh.hhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ie3 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	d4ie3a_	A:
1b	d4ie3b_	B:
1c	d4ie3c_	C:

(no "CATH Domain" information available for 4IE3)

(no "Pfam Domain" information available for 4IE3)

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 16)

Sites (16, 16)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

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