4N07 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE GLUA2 LIGAND-BINDING DOMAIN (S1S2J-L483Y-N754S) IN COMPLEX WITH GLUTAMATE AND BPAM-344 AT 1.87 A RESOLUTION

Authors :   A. B. Noerholm, K. Frydenvang, J. S. Kastrup

Date :   01 Oct 13 (Deposition) - 20 Nov 13 (Release) - 19 Mar 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.87

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

Keywords :   Ampa Receptor Ligand-Binding Domain, Glua2 S1S2J-L483Y-N754S, Bpam- 344 Allosteric Modulation, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. B. Nrholm, P. Francotte, L. Olsen, C. Krintel, K. Frydenvang, E. Goffin, S. Challal, L. Danober, I. Botez-Pop, P. Lestage, B. Pirotte, J. S. Kastrup
Synthesis, Pharmacological And Structural Characterization, And Thermodynamic Aspects Of Glua2-Positive Allosteric Modulators With A 3, 4-Dihydro-2H-1, 2, 4-Benzothiadiazine 1, 1-Dioxide Scaffold.
J. Med. Chem. V. 56 8736 2013
PubMed-ID: 24131202 | Reference-DOI: 10.1021/JM4012092

Molecule 1 - GLUTAMATE RECEPTOR 2
	Chains	:	A, B, C
	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	:	UNP RESIDUES 413-527, UNP REISDUES 653-796
	Gene	:	GLUR2, GRIA2
	Mutation	:	YES
	Organism Common	:	RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Strain	:	RAT
	Synonym	:	GLUR-2, AMPA-SELECTIVE GLUTAMATE RECEPTOR 2, GLUR-B, GLUR- K2, GLUTAMATE RECEPTOR IONOTROPIC, AMPA 2, GLUA2

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 36)

No.	Name	Count	Type	Full Name
1	2J9	3	Ligand/Ion	4-CYCLOPROPYL-7-FLUORO-3,4-DIHYDRO-2H-1,2,4-BENZOTHIADIAZINE 1,1-DIOXIDE
2	ACT	13	Ligand/Ion	ACETATE ION
3	CAC	1	Ligand/Ion	CACODYLATE ION
4	GLU	3	Mod. Amino Acid	GLUTAMIC ACID
5	GOL	6	Ligand/Ion	GLYCEROL
6	ZN	10	Ligand/Ion	ZINC ION

Biological Unit 1 (5, 26)

No.	Name	Count	Type	Full Name
1	2J9	2	Ligand/Ion	4-CYCLOPROPYL-7-FLUORO-3,4-DIHYDRO-2H-1,2,4-BENZOTHIADIAZINE 1,1-DIOXIDE
2	ACT	12	Ligand/Ion	ACETATE ION
3	CAC	2	Ligand/Ion	CACODYLATE ION
4	GLU	2	Mod. Amino Acid	GLUTAMIC ACID
5	GOL	8	Ligand/Ion	GLYCEROL
6	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (4, 13)

No.	Name	Count	Type	Full Name
1	2J9	2	Ligand/Ion	4-CYCLOPROPYL-7-FLUORO-3,4-DIHYDRO-2H-1,2,4-BENZOTHIADIAZINE 1,1-DIOXIDE
2	ACT	7	Ligand/Ion	ACETATE ION
3	CAC	-1	Ligand/Ion	CACODYLATE ION
4	GLU	2	Mod. Amino Acid	GLUTAMIC ACID
5	GOL	2	Ligand/Ion	GLYCEROL
6	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (36, 36)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS A:104 , PRO A:105 , PHE A:106 , MET A:107 , SER A:108 , SER A:217 , LYS A:218 , GLY A:219 , SER A:242	BINDING SITE FOR RESIDUE 2J9 A 301
02	AC2	SOFTWARE	TYR A:61 , PRO A:89 , LEU A:90 , THR A:91 , ARG A:96 , GLY A:141 , SER A:142 , THR A:143 , GLU A:193 , HOH A:401 , HOH A:404 , HOH A:412	BINDING SITE FOR RESIDUE GLU A 302
03	AC3	SOFTWARE	ARG A:180 , SER A:184 , LYS A:187 , TYR A:188	BINDING SITE FOR RESIDUE ACT A 303
04	AC4	SOFTWARE	ASN A:214 , ASP A:216 , ASP A:248	BINDING SITE FOR RESIDUE ACT A 304
05	AC5	SOFTWARE	LYS A:144 , PHE A:170 , ZN A:311 , CAC A:313	BINDING SITE FOR RESIDUE ACT A 305
06	AC6	SOFTWARE	LYS A:20 , HIS A:23 , GLU A:30 , ZN A:309 , HIS C:23 , HOH C:500	BINDING SITE FOR RESIDUE ACT A 306
07	AC7	SOFTWARE	LYS A:204 , GLU A:260 , HOH A:663	BINDING SITE FOR RESIDUE ACT A 307
08	AC8	SOFTWARE	LYS A:4 , ASP A:84	BINDING SITE FOR RESIDUE ACT A 308
09	AC9	SOFTWARE	HIS A:23 , GLU A:30 , ACT A:306 , HIS C:23	BINDING SITE FOR RESIDUE ZN A 309
10	BC1	SOFTWARE	ASP A:156 , HOH A:618	BINDING SITE FOR RESIDUE ZN A 310
11	BC2	SOFTWARE	ACT A:305 , CAC A:313 , HOH A:623 , HOH A:655	BINDING SITE FOR RESIDUE ZN A 311
12	BC3	SOFTWARE	GLU A:42 , HIS A:46 , LEU A:241 , HOH A:659 , GLU B:166	BINDING SITE FOR RESIDUE ZN A 312
13	BC4	SOFTWARE	ARG A:163 , ALA A:165 , GLU A:166 , SER A:168 , ACT A:305 , ZN A:311 , HOH A:655 , GLU B:42 , HIS B:46 , ZN B:305	BINDING SITE FOR RESIDUE CAC A 313
14	BC5	SOFTWARE	LEU A:127 , SER A:128 , GLN A:130 , TYR A:135	BINDING SITE FOR RESIDUE GOL A 314
15	BC6	SOFTWARE	PRO A:120 , GLU A:132 , ILE A:133 , GLY A:186 , LYS A:187 , HOH A:514 , HOH A:650	BINDING SITE FOR RESIDUE GOL A 315
16	BC7	SOFTWARE	GLU A:201 , LYS A:210 , HOH A:653	BINDING SITE FOR RESIDUE GOL A 316
17	BC8	SOFTWARE	GLU A:122 , SER A:123 , ASP A:126 , HOH A:613 , HOH A:664	BINDING SITE FOR RESIDUE GOL A 317
18	BC9	SOFTWARE	PRO B:105 , MET B:107 , SER B:108 , SER B:217 , LYS B:218 , GLY B:219 , LYS C:104 , PRO C:105 , PHE C:106 , MET C:107 , SER C:108 , SER C:242 , LEU C:247 , 2J9 C:301	BINDING SITE FOR RESIDUE 2J9 B 301
19	CC1	SOFTWARE	TYR B:61 , PRO B:89 , LEU B:90 , THR B:91 , ARG B:96 , LEU B:138 , GLY B:141 , SER B:142 , THR B:143 , GLU B:193 , HOH B:404 , HOH B:418 , HOH B:500	BINDING SITE FOR RESIDUE GLU B 302
20	CC2	SOFTWARE	MET B:19 , HIS B:23 , ZN B:306 , ASP C:65 , ASP C:67 , THR C:68	BINDING SITE FOR RESIDUE ACT B 303
21	CC3	SOFTWARE	ARG B:180 , LYS B:187 , TYR B:188	BINDING SITE FOR RESIDUE ACT B 304
22	CC4	SOFTWARE	GLU A:166 , CAC A:313 , GLU B:42 , HIS B:46	BINDING SITE FOR RESIDUE ZN B 305
23	CC5	SOFTWARE	HIS B:23 , ACT B:303 , HOH B:540 , ASP C:65	BINDING SITE FOR RESIDUE ZN B 306
24	CC6	SOFTWARE	ASP B:156 , ARG B:163	BINDING SITE FOR RESIDUE ZN B 307
25	CC7	SOFTWARE	ASP B:248 , ASN C:214	BINDING SITE FOR RESIDUE GOL B 308
26	CC8	SOFTWARE	GLU B:201 , LYS B:210	BINDING SITE FOR RESIDUE GOL B 309
27	CC9	SOFTWARE	LYS B:104 , PRO B:105 , PHE B:106 , MET B:107 , SER B:108 , SER B:242 , LEU B:247 , 2J9 B:301 , PRO C:105 , MET C:107 , SER C:108 , SER C:217 , LYS C:218 , GLY C:219	BINDING SITE FOR RESIDUE 2J9 C 301
28	DC1	SOFTWARE	TYR C:61 , PRO C:89 , LEU C:90 , THR C:91 , ARG C:96 , LEU C:138 , GLY C:141 , SER C:142 , THR C:143 , GLU C:193 , TYR C:220 , HOH C:407 , HOH C:419 , HOH C:495	BINDING SITE FOR RESIDUE GLU C 302
29	DC2	SOFTWARE	GLY C:62 , THR C:93 , ARG C:96 , ARG C:149 , HOH C:455 , HOH C:557	BINDING SITE FOR RESIDUE ACT C 303
30	DC3	SOFTWARE	GLU C:201	BINDING SITE FOR RESIDUE ACT C 304
31	DC4	SOFTWARE	GLU C:42 , LYS C:45 , HIS C:46 , ZN C:308 , HOH C:525 , HOH C:586 , HOH C:603	BINDING SITE FOR RESIDUE ACT C 305
32	DC5	SOFTWARE	ASN B:214 , ASP C:248	BINDING SITE FOR RESIDUE ACT C 306
33	DC6	SOFTWARE	GLU B:24 , ALA C:63 , ARG C:64 , ASN C:72 , ASP C:139 , SER C:140 , ZN C:310	BINDING SITE FOR RESIDUE ACT C 307
34	DC7	SOFTWARE	GLU C:42 , HIS C:46 , ACT C:305 , HOH C:603	BINDING SITE FOR RESIDUE ZN C 308
35	DC8	SOFTWARE	ASP C:156 , HOH C:544 , HOH C:556	BINDING SITE FOR RESIDUE ZN C 309
36	DC9	SOFTWARE	GLU B:24 , ASP C:139 , SER C:140 , ACT C:307 , HOH C:574	BINDING SITE FOR RESIDUE ZN C 310

Asymmetric Unit

No.	Residues
1	A:206	-	A:261
2	B:206	-	B:261
3	C:206	-	C: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 B:14	-	Pro B:15
5	Glu B:166	-	Pro B:167
6	Lys B:204	-	Pro B:205
7	Ser C:14	-	Pro C:15
8	Glu C:166	-	Pro C:167
9	Lys C:204	-	Pro C:205

(no "SAP(SNP)/Variant" information available for 4N07)

(no "PROSITE Motif" information available for 4N07)

(no "Exon" information available for 4N07)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains d4n07a_ A: 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....eeee...hhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhh...eeeeeehhhhhhhhh.....eeee......eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n07 A   1 GANKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITYVREEVIDFSKPFMSLGISIMIKKGTPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLSEQGLLDKLKNKWWYDKGECG 262
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260

Chain B from PDB  Type:PROTEIN  Length:260
                                                                                                                                                                                                                                                                                                    
               SCOP domains d4n07b_ B: 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
                 4n07 B   2 ANKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITYVREEVIDFSKPFMSLGISIMIKKGTPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLSEQGLLDKLKNKWWYDKGEC 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

Chain C from PDB  Type:PROTEIN  Length:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains d4n07c_ C: 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......hhhhhh.eee....eee.eeeeee......hhhhhhh....eeee...hhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhh...eeeeeehhhhhhhhh.....eeee......eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n07 C   1 GANKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITYVREEVIDFSKPFMSLGISIMIKKGTPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLSEQGLLDKLKNKWWYDKGECG 262
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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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	d4n07a_	A:
1b	d4n07b_	B:
1c	d4n07c_	C:

(no "CATH Domain" information available for 4N07)

(no "Pfam Domain" information available for 4N07)

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

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3tdj	CRYSTAL STRUCTURE OF THE GLUA2 LIGAND-BINDING DOMAIN (S1S2J -L483Y-N754S) IN COMPLEX WITH GLUTAMATE AND BPAM-97 AT 1.95 A RESOLUTION

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 36)

Sites (36, 36)

SS Bonds (3, 3)

Cis Peptide Bonds (9, 9)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (1, 3)

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Gene Ontology (49, 49)

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