4ISU - 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)

Biological Unit 5 (Jmol Viewer)

Biological Unit 6 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE GLUA2 LIGAND-BINDING DOMAIN (S1S2J) IN COMPLEX WITH THE ANTAGONIST (2R)-IKM-159 AT 2.3A RESOLUTION.

Authors :   L. Juknaite, K. Frydenvang, J. S. Kastrup

Date :   17 Jan 13 (Deposition) - 20 Mar 13 (Release) - 22 May 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,C  (1x)
Biol. Unit 2: B,D  (1x)
Biol. Unit 3: A  (1x)
Biol. Unit 4: D  (1x)
Biol. Unit 5: C  (1x)
Biol. Unit 6: B  (1x)

Keywords :   Ampa Receptor Ligand-Binding Domain, Glur2-S1S2J, Antagonist, Membrane Protein, Membrane Protein-Antagonist Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Juknaite, Y. Sugamata, K. Tokiwa, Y. Ishikawa, S. Takamizawa, A. Eng, R. Sakai, D. S. Pickering, K. Frydenvang, G. T. Swanson, J. S. Kastrup, M. Oikawa
Studies On An (S)-2-Amino-3-(3-Hydroxy-5-Methyl-4-Isoxazolyl)Propionic Acid (Ampa) Receptor Antagonist Ikm-159: Asymmetric Synthesis, Neuroactivity, And Structural Characterization.
J. Med. Chem. V. 56 2283 2013
PubMed-ID: 23432124 | Reference-DOI: 10.1021/JM301590Z

Molecule 1 - GLUTAMATE RECEPTOR 2
	Chains	:	A, D, C, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-22B(+)
	Expression System Strain	:	ORIGAMI B (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	LIGAND-BINDING DOMAIN
	Gene	:	GLUR2, GRIA2
	Organism Common	:	BROWN RAT,RAT,RATS
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	GLUR-2, AMPA-SELECTIVE GLUTAMATE RECEPTOR 2, GLUR-B, GLUR- K2, GLUTAMATE RECEPTOR IONOTROPIC, AMPA 2, GLUA2

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D
Biological Unit 3 (1x)	:	A
Biological Unit 4 (1x)	:				D
Biological Unit 5 (1x)	:			C
Biological Unit 6 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 16)

No.	Name	Count	Type	Full Name
1	CL	8	Ligand/Ion	CHLORIDE ION
2	IKM	2	Ligand/Ion	(4AS,5AR,6R,8AS,8BS)-5A-(CARBOXYMETHYL)-8-OXO-2,4A,5A,6,7,8,8A,8B-OCTAHYDRO-1H-PYRROLO[3',4':4,5]FURO[3,2-B]PYRIDINE-6-CARBOXYLIC ACID
3	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	IKM	1	Ligand/Ion	(4AS,5AR,6R,8AS,8BS)-5A-(CARBOXYMETHYL)-8-OXO-2,4A,5A,6,7,8,8A,8B-OCTAHYDRO-1H-PYRROLO[3',4':4,5]FURO[3,2-B]PYRIDINE-6-CARBOXYLIC ACID
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	IKM	1	Ligand/Ion	(4AS,5AR,6R,8AS,8BS)-5A-(CARBOXYMETHYL)-8-OXO-2,4A,5A,6,7,8,8A,8B-OCTAHYDRO-1H-PYRROLO[3',4':4,5]FURO[3,2-B]PYRIDINE-6-CARBOXYLIC ACID
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	IKM	1	Ligand/Ion	(4AS,5AR,6R,8AS,8BS)-5A-(CARBOXYMETHYL)-8-OXO-2,4A,5A,6,7,8,8A,8B-OCTAHYDRO-1H-PYRROLO[3',4':4,5]FURO[3,2-B]PYRIDINE-6-CARBOXYLIC ACID
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	IKM	-1	Ligand/Ion	(4AS,5AR,6R,8AS,8BS)-5A-(CARBOXYMETHYL)-8-OXO-2,4A,5A,6,7,8,8A,8B-OCTAHYDRO-1H-PYRROLO[3',4':4,5]FURO[3,2-B]PYRIDINE-6-CARBOXYLIC ACID
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 5 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	IKM	-1	Ligand/Ion	(4AS,5AR,6R,8AS,8BS)-5A-(CARBOXYMETHYL)-8-OXO-2,4A,5A,6,7,8,8A,8B-OCTAHYDRO-1H-PYRROLO[3',4':4,5]FURO[3,2-B]PYRIDINE-6-CARBOXYLIC ACID
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 6 (2, 3)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	IKM	1	Ligand/Ion	(4AS,5AR,6R,8AS,8BS)-5A-(CARBOXYMETHYL)-8-OXO-2,4A,5A,6,7,8,8A,8B-OCTAHYDRO-1H-PYRROLO[3',4':4,5]FURO[3,2-B]PYRIDINE-6-CARBOXYLIC ACID
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TYR A:61 , PRO A:89 , THR A:91 , ARG A:96 , LEU A:138 , GLY A:141 , SER A:142 , THR A:174 , GLU A:193 , TYR A:220 , HOH A:510	BINDING SITE FOR RESIDUE IKM A 301
02	AC2	SOFTWARE	HIS A:23 , LYS A:144 , ARG A:148	BINDING SITE FOR RESIDUE SO4 A 302
03	AC3	SOFTWARE	THR A:174	BINDING SITE FOR RESIDUE CL A 303
04	AC4	SOFTWARE	SER A:194 , GLU A:198	BINDING SITE FOR RESIDUE CL A 304
05	AC5	SOFTWARE	ARG D:96 , SER D:142	BINDING SITE FOR RESIDUE SO4 D 301
06	AC6	SOFTWARE	SER D:194 , GLU D:198	BINDING SITE FOR RESIDUE CL D 303
07	AC7	SOFTWARE	HIS C:23 , LYS C:144 , ARG C:148 , ARG C:163	BINDING SITE FOR RESIDUE SO4 C 301
08	AC8	SOFTWARE	TYR C:61 , THR C:91 , ARG C:96 , SER C:142	BINDING SITE FOR RESIDUE SO4 C 302
09	AC9	SOFTWARE	GLU C:198	BINDING SITE FOR RESIDUE CL C 303
10	BC1	SOFTWARE	SER C:140 , ARG C:148	BINDING SITE FOR RESIDUE CL C 304
11	BC2	SOFTWARE	TYR B:61 , PRO B:89 , THR B:91 , ARG B:96 , LEU B:138 , GLY B:141 , SER B:142 , THR B:174 , GLU B:193 , TYR B:220 , HOH B:454 , HOH B:466 , HOH B:503	BINDING SITE FOR RESIDUE IKM B 301
12	BC3	SOFTWARE	LYS B:144 , ARG B:148 , ARG B:163 , HIS D:23	BINDING SITE FOR RESIDUE SO4 B 302
13	BC4	SOFTWARE	HIS B:23 , LYS D:144 , ARG D:148 , TRP D:159	BINDING SITE FOR RESIDUE SO4 B 303
14	BC5	SOFTWARE	THR B:174	BINDING SITE FOR RESIDUE CL B 304
15	BC6	SOFTWARE	SER B:194 , GLU B:198	BINDING SITE FOR RESIDUE CL B 305

Asymmetric Unit

No.	Residues
1	A:206	-	A:261
2	B:206	-	B:261
3	C:206	-	C:261
4	D:206	-	D:261

Asymmetric Unit

No.	Residues
1	Ser A:14	-	Pro A:15
2	Glu A:166	-	Pro A:167
3	Lys A:204	-	Pro A:205
4	Ser D:14	-	Pro D:15
5	Glu D:166	-	Pro D:167
6	Lys D:204	-	Pro D:205
7	Ser C:14	-	Pro C:15
8	Glu C:166	-	Pro C:167
9	Lys C:204	-	Pro C:205
10	Ser B:14	-	Pro B:15
11	Glu B:166	-	Pro B:167
12	Lys B:204	-	Pro B:205

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

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

(no "Exon" information available for 4ISU)

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:258
                                                                                                                                                                                                                                                                                                  
               SCOP domains d4isua_ A: Glutamate receptor ligand binding core                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee.......ee..hhhhhhhhh.eehhhhhhhhhhhhh...eeeeee................hhhhhhhhh....ee......hhhhhh.eee....eee.eeeeee......hhhhhhh....eee....hhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhh...eeeeeehhhhhhhhh.....eeee......eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4isu A   4 KTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKGTPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLNEQGLLDKLKNKWWYDKGEC 261
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253

Chain B from PDB  Type:PROTEIN  Length:259
                                                                                                                                                                                                                                                                                                   
               SCOP domains d4isub_ B: Glutamate receptor ligand binding core                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......ee..hhhhhhhhh.eehhhhhhhhhhhhhhh.eeeeee................hhhhhhhhh....ee......hhhhhh.eee....eee.eeeeee......hhhhhhh....eee....hhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhh....eeeeeehhhhhhhhh.....eeee......eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4isu B   4 KTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKGTPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLNEQGLLDKLKNKWWYDKGECG 262
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253

Chain C from PDB  Type:PROTEIN  Length:259
                                                                                                                                                                                                                                                                                                   
               SCOP domains d4isuc_ C: Glutamate receptor ligand binding core                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.......ee.......hhhh.eehhhhhhhhhhhhhhh..eeeee................hhhhhhhhh....ee......hhhhhh.eee....eee.eeeeee......hhhhhhh....eee....hhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhh...eeeeeehhhhhhhh......eeee......eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4isu C   4 KTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKGTPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLNEQGLLDKLKNKWWYDKGECG 262
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253

Chain D from PDB  Type:PROTEIN  Length:260
                                                                                                                                                                                                                                                                                                    
               SCOP domains d4isud_ D: Glutamate receptor ligand binding core                                                                                                                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.......ee..hhhhhhhhh.eehhhhhhhhhhhhhhh..eeeee................hhhhhhhhh....ee......hhhhhhheee....eee.eeeeee......hhhhhhh....eee....hhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhh...eeeeeehhhhhhhhh.....eeee......eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4isu D   2 ANKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKGTPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLNEQGLLDKLKNKWWYDKGEC 261
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Periplasmic binding protein-like II (813)

Superfamily: Periplasmic binding protein-like II (813)

Family: Phosphate binding protein-like (463)

Protein domain: Glutamate receptor ligand binding core (127)

Norway rat (Rattus norvegicus), GluR2 [TaxId: 10116] (115)

1a	d4isua_	A:
1b	d4isub_	B:
1c	d4isuc_	C:
1d	d4isud_	D:

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
		Glu A:166 - Pro A:167	[ RasMol ]
		Glu B:166 - Pro B:167	[ RasMol ]
		Glu C:166 - Pro C:167	[ RasMol ]
		Glu D:166 - Pro D:167	[ RasMol ]
		Lys A:204 - Pro A:205	[ RasMol ]
		Lys B:204 - Pro B:205	[ RasMol ]
		Lys C:204 - Pro C:205	[ RasMol ]
		Lys D:204 - Pro D:205	[ RasMol ]
		Ser A:14 - Pro A:15	[ RasMol ]
		Ser B:14 - Pro B:15	[ RasMol ]
		Ser C:14 - Pro C:15	[ RasMol ]
		Ser D:14 - Pro D:15	[ RasMol ]

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Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 16)

Sites (15, 15)

SS Bonds (4, 4)

Cis Peptide Bonds (12, 12)

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SAPs(SNPs)/Variants (0, 0)

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