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(-) Description

Title :  CRYSTAL STRUCTURE OF GLUN1/GLUN2A NMDA RECEPTOR AGONIST BINDING DOMAINS WITH GLYCINE AND ANTAGONIST, PHENYL-ACEPC
 
Authors :  T. -C. Mou, P. Conti, A. Pinto, L. Tamborini, S. R. Sprang, K. B. Hansen
Date :  26 Aug 15  (Deposition) - 14 Sep 16  (Release) - 14 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transport Protein, Receptor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. -C. Mou, S. R. Sprang, K. B. Hansen
Crystal Structure Of Glun1/Glun2A Nmda Receptor Agonist Binding Domains With Glycine And Antagonist, Phenyl-Acepc
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GLUTAMATE RECEPTOR IONOTROPIC, NMDA 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 394-544, 663-800
    Gene: GRIN1, NMDAR1
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: GLUN1,GLUTAMATE [NMDA] RECEPTOR SUBUNIT ZETA-1,N-METHYL-D- ASPARTATE RECEPTOR SUBUNIT NR1,NMD-R1
 
Molecule 2 - GLUTAMATE RECEPTOR IONOTROPIC, NMDA 2A
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 402-539, 661-802
    Gene: GRIN2A
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: GLUN2A,GLUTAMATE [NMDA] RECEPTOR SUBUNIT EPSILON-1,N-METHYL D-ASPARTATE RECEPTOR SUBTYPE 2A,NR2A

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
15E01Ligand/Ion5-[(2R)-2-AMINO-2-CARBOXYETHYL]-1-PHENYL-1H-PYRAZOLE-3-CARBOXYLIC ACID
2GLY1Mod. Amino AcidGLYCINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:92 , PRO A:124 , LEU A:125 , THR A:126 , ARG A:131 , SER A:179 , SER A:180 , ASP A:224binding site for residue GLY A 1001
2AC2SOFTWAREHIS B:88 , SER B:114 , THR B:116 , ARG B:121 , THR B:134 , GLY B:135 , ILE B:136 , GLY B:172 , SER B:173 , THR B:174 , TYR B:214 , ASP B:215 , HOH B:407 , HOH B:408 , HOH B:421binding site for residue 5E0 B 301

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:28 -A:62
2A:44 -A:63
3B:32 -B:58
4B:39 -B:59
5B:229 -B:284

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Glu A:14 -Pro A:15
2Ala B:17 -Pro B:18
3Ser B:161 -Pro B:162

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DEX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DEX)

(-) Exons   (0, 0)

(no "Exon" information available for 5DEX)

(-) Sequences/Alignments

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:270
                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.......eee.....................eeeee..eeeeeehhhhhhhhhhhhhh...eeeee........eee...eeehhhhhhhhh....eeeeeee.hhhhhh.eee....eeeeeeeeee.........hhhhhh......ee....hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh....eeeeehhhhhhhhhhh..eee.....eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5dex A    5 RLKIVTIHQEPFVYVKPTMSDGTCKEEFTVNGDPVKKVICTGPTVPQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKGTRITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRG 1001
                                    14        24        34        44  ||    64        74        84        94   ||  107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277      1001
                                                                     47|                                      98|                                                                                                                                                                                     286|
                                                                      58                                      102                                                                                                                                                                                     1001


Chain B from PDB  Type:PROTEIN  Length:279
                                                                                                                                                                                                                                                                                                                        
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......eeee...........eeeeeeee.......eeeeeeeeehhhhhhhhhhhhhh..eeeeee........ee..eehhhhhhhhh....ee......hhhhhh.eee....eeeeeeeeee.........hhhhhhhhhh.....ee....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh....eeeeehhhhhhhhhh.....eee.hhhhheeeeee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5dex B    6 DNHLSIVTLEEAPFVIVEDIDPTETCVRNTVPCRKFVKINNSTNEGMNVKKCCKGFCIDILKKLSRTVKFTYDLYLVTNGKHGKKVNNVWNGMIGEVVYQRAVMAVGSLTINEERSEVVDFSVPFVETGISVMVSRGTQVTGLSDKKFQRPHDYSPPFRFGTVPNGSTERNIRNNYPYMHQYMTRFNQRGVEDALVSLKTGKLDAFIYDAAVLNYKAGRDEGCKLVTIGSGYIFATTGYGIALQKGSPWKRQIDLALLQFVGDGEMEELETLWLTGICH  285
                                    15        25 ||     36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276         
                                                27|                                                                                                                                                                                                                                                                
                                                 29
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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  (0, 0)

(no "SCOP Domain" information available for 5DEX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DEX)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DEX)

(-) Gene Ontology  (79, 116)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NMDE1_RAT | Q00959: 2a5s 2a5t 4jwx 4nf4 4nf5 4nf6 4nf8 5ddn 5ddx 5de4 5i56 5i57 5i58 5i59 5jty 5tpw 5tq0 5tq2 5vih 5vii 5vij
        NMDZ1_RAT | P35439: 1pb7 1pb8 1pb9 1pbq 1y1m 1y1z 1y20 2a5t 3q41 4kcc 4kfq 4nf4 4nf5 4nf6 4nf8 4pe5 5ddn 5ddx 5de4 5fxg 5fxh 5fxi 5fxj 5fxk 5i56 5i57 5i58 5i59 5jty 5u8c 5vih 5vii 5vij

(-) Related Entries Specified in the PDB File

5ddn 5ddx 5de4