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(-) Description

Title :  STRUCTURE OF THE HUMAN GLUN1/GLUN2A LBD IN COMPLEX WITH GNE0723
 
Authors :  H. J. A. Wallweber, P. J. Lupardus
Date :  08 Jun 16  (Deposition) - 13 Jul 16  (Release) - 13 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.44
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nmda, Receptor, Glutamate, Channel, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Volgraf, B. D. Sellers, Y. Jiang, G. Wu, C. Q. Ly, E. Villemure, R. M. Pastor, P. W. Yuen, A. Lu, X. Luo, M. Liu, S. Zhang, L. Sun, Y. Fu, P. J. Lupardus, H. J. Wallweber, B. M. Liederer, G. Deshmukh, E. Plise, S. Tay, P. Reynen, J. Herrington, A. Gustafson, Y. Liu, A. Dirksen, M. G. Dietz, Y. Liu, T. M. Wang, J. E. Hanson, D. Hackos, K. Scearce-Levie, J. B. Schwarz
Discovery Of Glun2A-Selective Nmda Receptor Positive Allosteric Modulators (Pams): Tuning Deactivation Kinetics Via Structure-Based Design.
J. Med. Chem. V. 59 2760 2016
PubMed-ID: 26919761  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B02010

(-) 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
16RV1Ligand/Ion(1~{R},2~{R})-2-[7-[[5-CHLORANYL-3-(TRIFLUOROMETHYL)PYRAZOL-1-YL]METHYL]-5-OXIDANYLIDENE-2-(TRIFLUOROMETHYL)-[1,3]THIAZOLO[3,2-A]PYRIMIDIN-3-YL]CYCLOPROPANE-1-CARBONITRILE
2ACT1Ligand/IonACETATE ION
3GLU1Mod. Amino AcidGLUTAMIC ACID
4GLY1Mod. 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:407 , HOH A:414 , HOH A:453binding site for residue GLU A 302
3AC3SOFTWAREILE 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 , ARG B:248 , GLY B:250 , LEU B:270 , HIS B:273binding site for residue 6RV A 303
4AC4SOFTWAREPHE B:93 , PRO B:125 , LEU B:126 , THR B:127 , ARG B:132 , SER B:180 , SER B:181 , ASP B:225binding site for residue GLY B 301

(-) 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 5KDT)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5KDT)

(-) 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:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......eeee..........eeeeeeee.......eeeeeeeeehhhhhhhhhhhhhh..eeeeee........ee..eehhhhhhhhh....ee......hhhhhh..ee....eeeeeeeeee.........hhhhhhhhhh.....ee....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh....eeeeehhhhhhhhhh.....eeehhhhh.eeeeee..ee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kdt A   5 DNHLSIVTLEEAPFVIVEDIDPETCVRNTVPCRKFVKINNSTNEGMNVKKCCKGFCIDILKKLSRTVKFTYDLYLVTNGKHGKKVNNVWNGMIGEVVYQRAVMAVGSLTINEERSEVVDFSVPFVETGISVMVSRGTQVTGLSDKKFQRPHDYSPPFRFGTVPNGSTERNIRNNYPYMHQYMTKFNQKGVEDALVSLKTGKLDAFIYDAAVLNYKAGRDEGCKLVTIGSGYIFATTGYGIALQKGSPWKRQIDLALLQFVGDGEMEELETLWLTGICH 284
                                    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:285
                                                                                                                                                                                                                                                                                                                             
               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..hhhhhhhhhh....hhhhhhhhhhh....eeeeehhhhhhhhh....eeeeeeeeeeeee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kdt B   3 MSTRLKIVTIHQEPFVYVKPTLSDGTCKEEFTVNGDPVKKVICTGPNDTSPGSPRHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKGTRITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQG 301
                                    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|                                                                                                                                                                                       289|
                                                                                                                           103                                                                                                                                                                                        301
   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 5KDT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (122, 165)

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_HUMAN | Q12879: 3nfl 5h8f 5h8h 5h8n 5h8q 5i2k 5i2n 5kcj 5tp9 5tpa
        NMDZ1_HUMAN | Q05586: 2hqw 2nr1 3bya 5h8f 5h8h 5h8n 5h8q 5i2k 5i2n 5kcj 5tp9 5tpa

(-) Related Entries Specified in the PDB File

5i2k 5i2n