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(-) Description

Title :  STRUCTURE OF THE HUMAN GLUN1/GLUN2A LBD IN COMPLEX WITH GNE6901
 
Authors :  H. J. A. Wallweber, P. J. Lupardus
Date :  06 Jun 16  (Deposition) - 13 Jul 16  (Release) - 13 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Grin1, Grin2A, Nmda Receptor, Glycine, Glutamate, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. H. Hackos, P. J. Lupardus, T. Grand, Y. Chen, T. M. Wang, P. Reynen, A. Gustafson, H. J. Wallweber, M. Volgraf, B. D. Sellers, J. B. Schwarz P. Paoletti, M. Sheng, Q. Zhou, J. E. Hanson
Positive Allosteric Modulators Of Glun2A-Containing Nmdars With Distinct Modes Of Action And Impacts On Circuit Function.
Neuron V. 89 983 2016
PubMed-ID: 26875626  |  Reference-DOI: 10.1016/J.NEURON.2016.01.016

(-) Compounds

Molecule 1 - GLUTAMATE RECEPTOR IONOTROPIC, NMDA 2A
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: LIGAND BINDING DOMAIN (UNP RESIDUES 401-539, GT LINKER, UNP RESIDUES 661-802)
    Gene: GRIN2A, NMDAR2A
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GLUN2A, GLUTAMATE [NMDA] RECEPTOR SUBUNIT EPSILON-1, N- METHYL D-ASPARTATE RECEPTOR SUBTYPE 2A, HNR2A
 
Molecule 2 - GLUTAMATE RECEPTOR IONOTROPIC, NMDA 1
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: LIGAND BINDING DOMAIN (UNP RESIDUES 415-565, GT LINKER, UNP RESIDUES 684-821)
    Gene: GRIN1, NMDAR1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GLUN1, GLUTAMATE [NMDA] RECEPTOR SUBUNIT ZETA-1, N-METHYL-D- ASPARTATE RECEPTOR SUBUNIT NR1, NMD-R1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 4)

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
16RM1Ligand/Ion7-[(4-FLUORANYLPHENOXY)METHYL]-3-[(1~{R},2~{R})-2-(HYDROXYMETHYL)CYCLOPROPYL]-2-METHYL-[1,3]THIAZOLO[3,2-A]PYRIMIDIN-5-ONE
2ACT1Ligand/IonACETATE ION
3GLU1Mod. Amino AcidGLUTAMIC ACID
4GLY1Mod. Amino AcidGLYCINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:39 , TYR A:80binding site for residue ACT A 301
2AC2SOFTWAREHIS A:87 , SER A:113 , LEU A:114 , THR A:115 , ARG A:120 , GLY A:171 , SER A:172 , THR A:173 , TYR A:213 , ASP A:214 , HOH A:432 , HOH A:477binding site for residue GLU A 302
3AC3SOFTWAREPHE B:93 , PRO B:125 , LEU B:126 , THR B:127 , ARG B:132 , SER B:180 , SER B:181 , ASP B:225 , PHE B:251binding site for residue GLY B 301
4AC4SOFTWAREILE A:116 , PRO A:129 , PHE A:130 , VAL A:131 , GLU A:132 , THR A:241 , THR A:242 , GLY A:243 , VAL A:266 , ILE B:128 , LYS B:140 , PRO B:141 , TYR B:144 , GLY B:250 , LEU B:270 , HIS B:273 , HOH B:462 , HOH B:467binding site for residue 6RM B 302

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:31 -A:57
2A:38 -A:58
3A:228 -A:283
4B:29 -B:63
5B:45 -B:64

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ala A:16 -Pro A:17
2Ser A:160 -Pro A:161
3Glu B:15 -Pro B:16

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5KCJ)

(-) 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:279
                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......eeee............eeeeeeee.......eeeeeeeeehhhhhhhhhhhhhhh.eeeeee........ee..eehhhhhhhhh....ee......hhhhhh..ee....eeeeeeeeee.........hhhhhhhhhh.....ee....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh....eeeeehhhhhhhhhhh....eeehhhhh.eeeeee..ee.....hhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kcj A   5 DNHLSIVTLEEAPFVIVEDIDPLTETCVRNTVPCRKFVKINNSTNEGMNVKKCCKGFCIDILKKLSRTVKFTYDLYLVTNGKHGKKVNNVWNGMIGEVVYQRAVMAVGSLTINEERSEVVDFSVPFVETGISVMVSRGTQVTGLSDKKFQRPHDYSPPFRFGTVPNGSTERNIRNNYPYMHQYMTKFNQKGVEDALVSLKTGKLDAFIYDAAVLNYKAGRDEGCKLVTIGSGYIFATTGYGIALQKGSPWKRQIDLALLQFVGDGEMEELETLWLTGIC 283
                                    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         


Chain B from PDB  Type:PROTEIN  Length:281
                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......eeee....................eeeeee..........eeeeeeehhhhhhhhhhhhhhh.eeeeee........eee...eeehhhhhhhhh....ee......hhhhhh.eee....eeeeeeeeee.........hhhhhh......ee....hhhhhhhhhh..hhhhhhhhh.....hhhhhhhhhhh....eeeeehhhhhhhhhhh..eeeeeeeeeeeee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kcj B   5 TRLKIVTIHQEPFVYVKPTLSDGTCKEEFTVNGDPVKKVICTGPNDTSPGSPRHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKGTRITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRG 301
                                    14        24        34        44        54        64        74        84        94    || 107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287|
                                                                                                                         99|                                                                                                                                                                                     287|
                                                                                                                         103                                                                                                                                                                                      301
   Legend:   → Mismatch (orange background)
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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 5KCJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (121, 163)

Asymmetric/Biological Unit(hide GO term definitions)

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  NMDE1_HUMAN | Q12879
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  NMDZ1_HUMAN | Q05586
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 Related Entries

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

UniProtKB/Swiss-Prot
        NMDE1_HUMAN | Q12879: 3nfl 5h8f 5h8h 5h8n 5h8q 5i2k 5i2n 5kdt 5tp9 5tpa
        NMDZ1_HUMAN | Q05586: 2hqw 2nr1 3bya 5h8f 5h8h 5h8n 5h8q 5i2k 5i2n 5kdt 5tp9 5tpa

(-) Related Entries Specified in the PDB File

5h8f 5h8h 5h8n 5h8q 5h8s