4IGT - JenaLib

Title :   CRYSTAL STRUCTURE OF THE GLUA2 LIGAND-BINDING DOMAIN (S1S2J) IN COMPLEX WITH THE AGONIST ZA302 AT 1.24A RESOLUTION

Authors :   A. P. Larsen, R. Venskutonyte, M. Gajhede, J. S. Kastrup, K. Frydenvang

Date :   18 Dec 12 (Deposition) - 06 Mar 13 (Release) - 03 Sep 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.24

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

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

Reference :   Z. Assaf, A. P. Larsen, R. Venskutonyte, L. Han, B. Abrahamsen, B. Nielsen, M. Gajhede, J. S. Kastrup, A. A. Jensen, D. S. Pickering, K. Frydenvang, T. Gefflaut, L. Bunch
Chemoenzymatic Synthesis Of New 2, 4-Syn-Functionalized (S)-Glutamate Analogues And Structure-Activity Relationship Studies At Ionotropic Glutamate Receptors And Excitatory Amino Acid Transporters.
J. Med. Chem. V. 56 1614 2013
PubMed-ID: 23414088 | Reference-DOI: 10.1021/JM301433M

Compounds

Molecule 1 - GLUTAMATE RECEPTOR 2
	Chains	:	A
	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, UNP RESIDUES 413-527, 653-796
	Gene	:	GLUR2, GRIA2
	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

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 9)

Sites (9, 9)

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:423 , TYR A:471 , PRO A:499 , LEU A:500 , THR A:501 , ARG A:506 , LEU A:671 , GLY A:674 , SER A:675 , THR A:676 , GLU A:726 , TYR A:753 , HOH A:914 , HOH A:919	BINDING SITE FOR RESIDUE 3ZA A 801
2	AC2	SOFTWARE	HIS A:456 , ARG A:705 , LYS A:773 , GLN A:777	BINDING SITE FOR RESIDUE SO4 A 802
3	AC3	SOFTWARE	LYS A:527 , GLU A:734 , GLN A:735 , CYS A:739 , CYS A:794 , HOH A:903 , HOH A:1108	BINDING SITE FOR RESIDUE SO4 A 803
4	AC4	SOFTWARE	LYS A:470 , ALA A:473 , ASN A:482 , SER A:673 , HOH A:1016 , HOH A:1097 , HOH A:1215 , HOH A:1229	BINDING SITE FOR RESIDUE SO4 A 804
5	AC5	SOFTWARE	GLU A:507 , ILE A:510 , HOH A:958	BINDING SITE FOR RESIDUE LI A 805
6	AC6	SOFTWARE	VAL A:509 , GLY A:651 , HOH A:933 , HOH A:969 , HOH A:1070 , HOH A:1220	BINDING SITE FOR RESIDUE GOL A 806
7	AC7	SOFTWARE	ILE A:480 , TYR A:490 , LYS A:526 , LYS A:718 , GLY A:719 , GOL A:808 , HOH A:931	BINDING SITE FOR RESIDUE GOL A 807
8	AC8	SOFTWARE	LYS A:492 , LYS A:526 , GOL A:807 , HOH A:951 , HOH A:1111	BINDING SITE FOR RESIDUE GOL A 808
9	AC9	SOFTWARE	SER A:518 , SER A:727 , THR A:728 , GLU A:731 , ASN A:747 , HOH A:1061	BINDING SITE FOR RESIDUE GOL A 809

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
	(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:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains d4igta_ 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....eee....hhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhh...eeeeeehhhhhhhhh.....eeee......eee..eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4igt A 411 GANKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKGTPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLNEQGLLDKLKNKWWYDKGECGS 796
                                   420       430       440       450       460       470       480       490       500       510       520      |653       663       673       683       693       703       713       723       733       743       753       763       773       783       793   
                                                                                                                                              527|                                                                                                                                                 
                                                                                                                                               651

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (49, 49)

Visualization

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	Sites
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		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
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		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Glu A:699 - Pro A:700	[ RasMol ]
		Lys A:737 - Pro A:738	[ RasMol ]
		Ser A:424 - Pro A:425	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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