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(-) Description

Title :  STRUCTURE OF THE HUMAN GLUN1/GLUN2A LBD IN COMPLEX WITH GNE3419
 
Authors :  H. J. A. Wallweber, P. J. Lupardus
Date :  23 Dec 15  (Deposition) - 24 Feb 16  (Release) - 24 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.23
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Glun1, Glun2A, Nmda, Receptor, 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. A. 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 1 2016
PubMed: search  |  Reference-DOI: 10.1016/J.NEURON.2016.01.016

(-) Compounds

Molecule 1 - GLUTAMATE RECEPTOR IONOTROPIC, NMDA 2A,GLUTAMATE RECEPTOR IONOTROPIC, NMDA 2A
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: 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,GLUTAMATE RECEPTOR IONOTROPIC, NMDA 1
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 394-544, GT LINKER, UNP RESIDUES 663-800
    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  (5, 5)

Asymmetric/Biological Unit (5, 5)
No.NameCountTypeFull Name
15YC1Ligand/Ion7-[[ETHYL(PHENYL)AMINO]METHYL]-2-METHYL-[1,3,4]THIADIAZOLO[3,2-A]PYRIMIDIN-5-ONE
2ACT1Ligand/IonACETATE ION
3CA1Ligand/IonCALCIUM ION
4GLU1Mod. Amino AcidGLUTAMIC ACID
5GLY1Mod. Amino AcidGLYCINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:39binding site for residue ACT A 301
2AC2SOFTWAREHIS A:87 , SER A:113 , THR A:115 , ARG A:120 , GLY A:171 , SER A:172 , THR A:173 , TYR A:213 , ASP A:214 , HOH A:420 , HOH A:438binding 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 302
4AC4SOFTWAREPRO A:129 , VAL A:131 , GLU A:132 , THR A:241 , THR A:242 , GLY A:243 , VAL A:266 , PRO B:141 , LYS B:143 , TYR B:144 , GLY B:250 , HIS B:273 , HOH B:416binding site for residue 5YC B 303

(-) 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 5H8H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5H8H)

(-) Exons   (0, 0)

(no "Exon" information available for 5H8H)

(-) 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:277
                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......eeee..........eeeeeeee.......eeeeeeeeehhhhhhhhhhhhhhh.eeeeee........ee..eehhhhhhhhh....ee......hhhhhhhhee....eeeeeeeeee.........hhhhhhhhhh.....ee....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh....eeeeehhhhhhhhhhhhhh.eeehhhhh.eeeeee..ee.....hhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h8h A   5 DNHLSIVTLEEAPFVIVEDIDPETCVRNTVPCRKFVKINNSTNEGMNVKKCCKGFCIDILKKLSRTVKFTYDLYLVTNGKHGKKVNNVWNGMIGEVVYQRAVMAVGSLTINEERSEVVDFSVPFVETGISVMVSRGTQVTGLSDKKFQRPHDYSPPFRFGTVPNGSTERNIRNNYPYMHQYMTKFNQKGVEDALVSLKTGKLDAFIYDAAVLNYKAGRDEGCKLVTIGSGYIFATTGYGIALQKGSPWKRQIDLALLQFVGDGEMEELETLWLTGIC 283
                                    14        24 ||     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       
                                                26|                                                                                                                                                                                                                                                              
                                                 29                                                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:282
                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ 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..hhhhhhhhh.....hhhhhhhhhhh....eeeeehhhhhhhhhhh..eeeeeeeeeeeee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5h8h B   3 MSTRLKIVTIHQEPFVYVKPTLSDGTCKEEFTVNGDPVKKVICTGPNDTSPGSPRHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKGTRITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVR 287
                                    12        22        32        42        52        62        72        82        92      |105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285  
                                                                                                                           99|                                                                                                                                                                                        
                                                                                                                           103
   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  (0, 0)

(no "SCOP Domain" information available for 5H8H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5H8H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5H8H)

(-) Gene Ontology  (122, 165)

Asymmetric/Biological Unit(hide GO term definitions)

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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 5h8n 5h8q 5i2k 5i2n 5kcj 5kdt 5tp9 5tpa
        NMDZ1_HUMAN | Q05586: 2hqw 2nr1 3bya 5h8f 5h8n 5h8q 5i2k 5i2n 5kcj 5kdt 5tp9 5tpa

(-) Related Entries Specified in the PDB File

5h8f 5h8n 5h8q 5h8r 5h8s