4KFQ - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE NMDA RECEPTOR GLUN1 LIGAND BINDING DOMAIN IN COMPLEX WITH 1-THIOXO-1,2-DIHYDRO-[1,2,4]TRIAZOLO[4,3-A]QUINOXALIN-4(5H)-ONE

Authors :   T. B. Steffensen, F. M. Tabrizi, M. Gajhede, J. S. Kastrup

Date :   27 Apr 13 (Deposition) - 09 Oct 13 (Release) - 01 Jul 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Membrane Protein, Ligand Binding Domain, Ionotropic Glutamate Receptor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Kvist, T. B. Steffensen, J. R. Greenwood, F. Mehrzad Tabrizi, K. B. Hansen, M. Gajhede, D. S. Pickering, S. F. Traynelis, J. S. Kastrup, H. Brauner-Osborne
Crystal Structure And Pharmacological Characterization Of A Novel N-Methyl-D-Aspartate (Nmda) Receptor Antagonist At Th Glun1 Glycine Binding Site.
J. Biol. Chem. V. 288 33124 2013
PubMed-ID: 24072709 | Reference-DOI: 10.1074/JBC.M113.480210
(for further references see the PDB file header)

Molecule 1 - GLUTAMATE RECEPTOR IONOTROPIC, NMDA 1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22C
	Expression System Strain	:	ORIGAMI B (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 394-554, 663-800
	Gene	:	GRIN1, GRIN1 OR NMDAR1, NMDAR1
	Organism Common	:	BROWN RAT,RAT,RATS
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Other Details	:	THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GLUN1. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUES 153 AND 154 OF THE STRUCTURE). THEREFORE, THE SEQUENCE MATCHES DISCONTINUOUSLY WITH THE REFERENCE DATABASE (394-554, 663-800)
	Synonym	:	GLUN1, GLUTAMATE [NMDA] RECEPTOR SUBUNIT ZETA-1, N-METHYL-D- ASPARTATE RECEPTOR SUBUNIT NR1, NMD-R1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 28)

No.	Name	Count	Type	Full Name
1	GOL	18	Ligand/Ion	GLYCEROL
2	KFQ	2	Ligand/Ion	1-SULFANYL[1,2,4]TRIAZOLO[4,3-A]QUINOXALIN-4(5H)-ONE
3	SO4	8	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 14)

No.	Name	Count	Type	Full Name
1	GOL	9	Ligand/Ion	GLYCEROL
2	KFQ	1	Ligand/Ion	1-SULFANYL[1,2,4]TRIAZOLO[4,3-A]QUINOXALIN-4(5H)-ONE
3	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 14)

No.	Name	Count	Type	Full Name
1	GOL	9	Ligand/Ion	GLYCEROL
2	KFQ	1	Ligand/Ion	1-SULFANYL[1,2,4]TRIAZOLO[4,3-A]QUINOXALIN-4(5H)-ONE
3	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (28, 28)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PHE A:92 , PRO A:124 , LEU A:125 , THR A:126 , ARG A:131 , SER A:180 , GOL A:302	BINDING SITE FOR RESIDUE KFQ A 301
02	AC2	SOFTWARE	THR A:126 , GLN A:144 , SER A:180 , ASP A:224 , KFQ A:301 , GOL A:307 , HOH A:551	BINDING SITE FOR RESIDUE GOL A 302
03	AC3	SOFTWARE	LYS A:91 , PHE A:92 , GLY A:93 , THR A:94 , GLN A:178 , SER A:179 , HOH A:590	BINDING SITE FOR RESIDUE GOL A 303
04	AC4	SOFTWARE	ALA A:206 , ALA A:207 , GOL A:306 , HOH A:451	BINDING SITE FOR RESIDUE GOL A 304
05	AC5	SOFTWARE	PRO A:21 , GLU A:243 , LEU A:244 , ARG A:247 , SO4 A:311	BINDING SITE FOR RESIDUE GOL A 305
06	AC6	SOFTWARE	HIS A:12 , GLU A:14 , GOL A:304	BINDING SITE FOR RESIDUE GOL A 306
07	AC7	SOFTWARE	PRO A:55 , LEU A:146 , TYR A:184 , GOL A:302 , HOH A:484 , HOH A:495 , HOH A:516 , HOH A:551	BINDING SITE FOR RESIDUE GOL A 307
08	AC8	SOFTWARE	THR A:33 , PRO A:38 , VAL A:39 , LYS A:40 , ASP A:69 , THR A:283 , TRP A:284	BINDING SITE FOR RESIDUE GOL A 308
09	AC9	SOFTWARE	HIS A:12 , GLY A:46 , PRO A:47 , ASP A:49 , GLN A:61 , LEU A:86 , HOH A:513	BINDING SITE FOR RESIDUE GOL A 309
10	BC1	SOFTWARE	LYS A:40 , LYS A:41 , ARG A:76	BINDING SITE FOR RESIDUE GOL A 310
11	BC2	SOFTWARE	ASN A:48 , SER A:51 , SER A:54 , ARG A:56 , VAL A:59 , PHE A:245 , PHE A:246 , ARG A:247 , GOL A:305 , HOH A:406 , HOH A:611	BINDING SITE FOR RESIDUE SO4 A 311
12	BC3	SOFTWARE	PRO A:55 , ARG A:56 , HIS A:57 , THR A:58 , ASN A:129	BINDING SITE FOR RESIDUE SO4 A 312
13	BC4	SOFTWARE	SER A:168 , HIS A:197 , LYS A:200 , HOH A:474 , HOH A:594	BINDING SITE FOR RESIDUE SO4 A 313
14	BC5	SOFTWARE	ARG A:186 , ARG A:187	BINDING SITE FOR RESIDUE SO4 A 314
15	BC6	SOFTWARE	PHE B:92 , PRO B:124 , LEU B:125 , THR B:126 , ARG B:131 , SER B:180 , GOL B:303 , GOL B:304	BINDING SITE FOR RESIDUE KFQ B 301
16	BC7	SOFTWARE	HIS B:12 , GLY B:46 , PRO B:47 , ASP B:49 , GLN B:61 , LEU B:86 , HOH B:468	BINDING SITE FOR RESIDUE GOL B 302
17	BC8	SOFTWARE	LYS B:91 , PHE B:92 , GLY B:93 , THR B:94 , GLN B:178 , KFQ B:301 , HOH B:512 , HOH B:562	BINDING SITE FOR RESIDUE GOL B 303
18	BC9	SOFTWARE	THR B:126 , GLN B:144 , SER B:180 , VAL B:181 , ASP B:224 , KFQ B:301 , HOH B:459	BINDING SITE FOR RESIDUE GOL B 304
19	CC1	SOFTWARE	ASP B:37 , PRO B:38 , LYS B:40 , ASP B:69 , TRP B:284	BINDING SITE FOR RESIDUE GOL B 305
20	CC2	SOFTWARE	HIS B:12 , GLN B:13 , GLU B:14 , HOH B:428	BINDING SITE FOR RESIDUE GOL B 306
21	CC3	SOFTWARE	PRO B:55 , HIS B:57 , THR B:58 , ASN B:129	BINDING SITE FOR RESIDUE GOL B 307
22	CC4	SOFTWARE	ARG B:186 , ARG B:187	BINDING SITE FOR RESIDUE GOL B 308
23	CC5	SOFTWARE	THR B:33 , VAL B:34 , THR B:283 , TRP B:284 , HOH B:571 , HOH B:590	BINDING SITE FOR RESIDUE GOL B 309
24	CC6	SOFTWARE	THR B:157 , GLY B:158 , ILE B:159 , ASN B:160	BINDING SITE FOR RESIDUE GOL B 310
25	CC7	SOFTWARE	ASN B:48 , SER B:51 , SER B:54 , ARG B:56 , PHE B:245 , PHE B:246 , ARG B:247 , HOH B:535	BINDING SITE FOR RESIDUE SO4 B 311
26	CC8	SOFTWARE	PHE A:32 , LYS B:152 , GLY B:153 , ARG B:155 , VAL B:239 , HOH B:444	BINDING SITE FOR RESIDUE SO4 B 312
27	CC9	SOFTWARE	PRO B:167 , SER B:168 , ASP B:169 , HIS B:197 , LYS B:200	BINDING SITE FOR RESIDUE SO4 B 313
28	DC1	SOFTWARE	GLN B:188	BINDING SITE FOR RESIDUE SO4 B 314

Asymmetric Unit

No.	Residues
1	A:28	-	A:62
2	A:44	-	A:63
3	A:236	-	A:290
4	B:28	-	B:62
5	B:44	-	B:63

Asymmetric Unit

No.	Residues
1	Glu A:14	-	Pro A:15
2	Glu B:14	-	Pro B:15

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

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

(no "Exon" information available for 4KFQ)

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:289
                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4kfqa_ A: N-methyl-D-aspartate receptor subunit 1                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.......eeee....................eeeeee..........eeeeeeehhhhhhhhhhhhhhh..eeeee........eee......eeehhhhhhhhh....ee......hhhhhh.eee....eeeeeeeeee.........hhhhhh......ee....hhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhhh....eeeeehhhhhhhhhh...eeeeeeeeeeeee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kfq A   4 TRLKIVTIHQEPFVYVKPTMSDGTCKEEFTVNGDPVKKVICTGPNDTSPGSPRHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKGTRITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQECDS 292
                                    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       263       273       283

Chain B from PDB  Type:PROTEIN  Length:282
                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4kfqb_ B: N-methyl-D-aspartate receptor subunit 1                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.......eeee....................eeeeee..........eeeeeeehhhhhhhhhhhhhhh..eeeee........eee......eeehhhhhhhhh....ee......hhhhhh..ee....eeeeeeeeee.........hhhhhh......ee....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh....eeeeehhhhhhhhhhh..eeeeeeeeeeeee..ee.....hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4kfq B   5 RLKIVTIHQEPFVYVKPTMSDGTCKEEFTVNGDPVKKVICTGPNDTSPGSPRHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKGTRITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVR 286
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284

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 Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

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: N-methyl-D-aspartate receptor subunit 1 (15)

Norway rat (Rattus norvegicus) [TaxId: 10116] (14)

1a	d4kfqa_	A:
1b	d4kfqb_	B:

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
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		Glu B:14 - Pro B:15	[ RasMol ]

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1pb7	CRYSTAL STRUCTURE OF THE NR1 LIGAND BINDING CORE IN COMPLEX WITH GLYCINE AT 1.35 ANGSTROMS RESOLUTION
1pb8	CRYSTAL STRUCTURE OF THE NR1 LIGAND BINDING CORE IN COMPLEX WITH D-SERINE AT 1.45 ANGSTROMS RESOLUTION
1pb9	CRYSTAL STRUCTURE OF THE NR1 LIGAND BINDING CORE IN COMPLEX WITH D-CYCLOSERINE AT 1.60 ANGSTROMS RESOLUTION
1pbq	CRYSTAL STRUCTURE OF THE NR1 LIGAND BINDING CORE IN COMPLEX WITH 5,7-DICHLOROKYNURENIC ACID (DCKA) AT 1.90 ANGSTROMS RESOLUTION

Description

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Ligands, Modified Residues, Ions (3, 28)

Sites (28, 28)

SS Bonds (5, 5)

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