4IY5 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE GLUA2 LIGAND-BINDING DOMAIN (S1S2J-L483Y-N754S) IN COMPLEX WITH GLUTAMATE AND CX516 AT 2.0 A RESOLUTION

Authors :   C. Krintel, K. Frydenvang, K. Harpsoe, M. Gajhede, J. S. Kastrup

Date :   28 Jan 13 (Deposition) - 09 Oct 13 (Release) - 09 Oct 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A,B

Keywords :   Ampa Receptor Ligand-Binding Domain, Glua2 S1S2J-L483Y-N754S, Cx516, Allosteric Modulation, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Krintel, K. Harpsoe, L. G. Zachariassen, D. Peters, K. Frydenvang, D. S. Pickering, M. Gajhede, J. S. Kastrup
Structural Analysis Of The Positive Ampa Receptor Modulator Cx516 And Me-Cx516 In Complex With The Glua2 Ligand-Binding Domain
Acta Crystallogr. , Sect. D V. 69 1645 2013
PubMed-ID: 23999288 | Reference-DOI: 10.1107/S0907444913011839
(for further references see the PDB file header)

Molecule 1 - GLUTAMATE RECEPTOR 2
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-22B(+)
	Expression System Strain	:	ORIGAMI B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	LIGAND BINDING DOMAIN, UNP RESIDUES 413-527, 653-796
	Gene	:	GLUR2, GRIA2
	Mutation	:	YES
	Organism Common	:	RAT, BROWN 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
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 14)

No.	Name	Count	Type	Full Name
1	CL	3	Ligand/Ion	CHLORIDE ION
2	CX5	1	Ligand/Ion	PIPERIDIN-1-YL(QUINOXALIN-6-YL)METHANONE
3	GLU	2	Mod. Amino Acid	GLUTAMIC ACID
4	GOL	3	Ligand/Ion	GLYCEROL
5	SO4	5	Ligand/Ion	SULFATE ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	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 , TYR A:220 , HOH A:402 , HOH A:403 , HOH A:427	BINDING SITE FOR RESIDUE GLU A 301
02	AC2	SOFTWARE	SER A:140 , LYS A:144 , ARG A:148 , HOH A:419 , HOH A:429 , HOH A:512	BINDING SITE FOR RESIDUE SO4 A 302
03	AC3	SOFTWARE	ARG A:148 , TRP A:159 , ARG A:163	BINDING SITE FOR RESIDUE GOL A 303
04	AC4	SOFTWARE	LYS A:82 , LYS A:116 , HOH A:442 , HOH A:684	BINDING SITE FOR RESIDUE SO4 A 304
05	AC5	SOFTWARE	LYS A:4 , THR A:5	BINDING SITE FOR RESIDUE CL A 305
06	AC6	SOFTWARE	PRO A:105 , PHE A:106 , MET A:107 , SER A:108 , SER A:217 , LYS A:218 , GLY A:219 , PRO B:105 , PHE B:106 , MET B:107 , SER B:108 , SER B:217 , LYS B:218 , GLY B:219 , HOH B:436 , HOH B:508	BINDING SITE FOR RESIDUE CX5 B 301
07	AC7	SOFTWARE	TYR B:61 , PRO B:89 , LEU B:90 , THR B:91 , ARG B:96 , GLY B:141 , SER B:142 , THR B:143 , GLU B:193 , HOH B:402 , HOH B:412 , HOH B:445	BINDING SITE FOR RESIDUE GLU B 302
08	AC8	SOFTWARE	LYS A:183 , ARG B:31 , HOH B:429 , HOH B:432 , HOH B:588 , HOH B:594	BINDING SITE FOR RESIDUE SO4 B 303
09	AC9	SOFTWARE	SER B:140 , LYS B:144 , ARG B:148 , HOH B:441 , HOH B:497 , HOH B:657	BINDING SITE FOR RESIDUE SO4 B 304
10	BC1	SOFTWARE	ARG B:148 , TRP B:159 , ARG B:163	BINDING SITE FOR RESIDUE GOL B 305
11	BC2	SOFTWARE	SER B:194 , THR B:195 , GLU B:198 , ASN B:214 , HOH B:589	BINDING SITE FOR RESIDUE GOL B 306
12	BC3	SOFTWARE	HOH A:536 , LYS B:21 , ASN B:22 , HIS B:23 , HOH B:409 , HOH B:578	BINDING SITE FOR RESIDUE SO4 B 307
13	BC4	SOFTWARE	GLN B:244	BINDING SITE FOR RESIDUE CL B 308
14	BC5	SOFTWARE	ARG B:163	BINDING SITE FOR RESIDUE CL B 309

Asymmetric/Biological Unit

No.	Residues
1	A:206	-	A:261
2	B:206	-	B:261

Asymmetric/Biological 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

(no "SAP(SNP)/Variant" information available for 4IY5)

(no "PROSITE Motif" information available for 4IY5)

(no "Exon" information available for 4IY5)

Asymmetric/Biological 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:264
                                                                                                                                                                                                                                                                                                        
               SCOP domains d4iy5a_ A: 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...eeeeeehhhhhhhh......eeee......eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4iy5 A   1 GANKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITYVREEVIDFSKPFMSLGISIMIKKGTPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLSEQGLLDKLKNKWWYDKGECGSE 301
                                    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  ||
                                                                                                                                                                                                                                                                                                263|
                                                                                                                                                                                                                                                                                                 301

Chain B from PDB  Type:PROTEIN  Length:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains d4iy5b_ 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....eeee...hhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhh...eeeeeehhhhhhhhh.....eeee......eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4iy5 B   1 GANKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITYVREEVIDFSKPFMSLGISIMIKKGTPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLSEQGLLDKLKNKWWYDKGECGS 263
                                    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

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/Biological 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	d4iy5a_	A:
1b	d4iy5b_	B:

(no "CATH Domain" information available for 4IY5)

(no "Pfam Domain" information available for 4IY5)

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CX5	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GLU	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]

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

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	4iy5
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	GRIA2_RAT \| P19491
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	GRIA2_RAT \| P19491
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

2al4	CRYSTAL STRUCTURE OF THE GLUA2 LIGAND BINDING CORE IN COMPLEX WITH CX614 AT 1.70 A RESOLUTION.
2al5	CRYSTAL STRUCTURE OF THE GLUA2 LIGAND BINDING CORE IN COMPLEX WITH ANIRACETAM AT 1.65 A RESOLUTION.
3tdj	CRYSTAL STRUCTURE OF THE NON-DESENSITIZING FLIP LIKE GLUA2 LIGAND BINDING CORE MUTANT (S1S2J-L483Y-L754S) IN COMPLEX WITH BPAM-97 AS WELL AS GLUTAMATE AT 1.95 A RESOLUTION
3tdk	CRYSTAL STRUCTURE OF THE NON-DESENSITIZING FLIP LIKE GLUA2 LIGAND BINDING CORE MUTANT (S1S2J-L483Y-L754S) IN COMPLEX WITH CYCLOTHIAZIDE (CTZ) AS WELL AS GLUTAMATE AT 1.45 A RESOLUTION
4iy6

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 14)

Sites (14, 14)

SS Bonds (2, 2)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (49, 49)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File