4IY6 - JenaLib

Title :   CRYSTAL STRUCTURE OF THE GLUA2 LIGAND-BINDING DOMAIN (S1S2J-L483Y-N754S) IN COMPLEX WITH GLUTAMATE AND ME-CX516 AT 1.72 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 :   1.72

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

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

Reference :   C. Krintel, K. Harpse, 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)

Compounds

Molecule 1 - GLUTAMATE RECEPTOR 2
	Chains	:	A
	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

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 7)

Sites (7, 7)

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:105 , MET A:107 , SER A:108 , SER A:217 , LYS A:218 , SER A:242 , HOH A:471	BINDING SITE FOR RESIDUE MQR A 301
2	AC2	SOFTWARE	HIS A:23 , GLU A:24 , LYS A:129 , GLN A:130 , THR A:131 , ILE A:133 , TYR A:161 , HOH A:487 , HOH A:535	BINDING SITE FOR RESIDUE MQS A 302
3	AC3	SOFTWARE	TYR A:80 , LYS A:116 , LYS A:117 , GLY A:118 , THR A:119 , PRO A:120 , LYS A:185 , GLY A:186 , LYS A:187 , HOH A:513	BINDING SITE FOR RESIDUE MQS A 303
4	AC4	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:401 , HOH A:430 , HOH A:457	BINDING SITE FOR RESIDUE GLU A 304
5	AC5	SOFTWARE	ARG A:148 , TRP A:159 , ARG A:163 , HOH A:540	BINDING SITE FOR RESIDUE GOL A 305
6	AC6	SOFTWARE	SER A:140 , LYS A:144 , ARG A:148 , HOH A:459 , HOH A:478 , HOH A:649	BINDING SITE FOR RESIDUE SO4 A 306
7	AC7	SOFTWARE	LYS A:82 , LYS A:116 , HOH A:586 , HOH A:726 , HOH A:743	BINDING SITE FOR RESIDUE SO4 A 307

SS Bonds (1, 1)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:264
                                                                                                                                                                                                                                                                                                        
               SCOP domains d4iy6a_ 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...eeeeeehhhhhhhhh.....eeee......eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4iy6 A   1 GANKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITYVREEVIDFSKPFMSLGISIMIKKGTPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLSEQGLLDKLKNKWWYDKGECGSE 304
                                    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|
                                                                                                                                                                                                                                                                                                 304

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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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (49, 49)

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

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