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(-) Description

Title :  STRUCTURE OF THE HUMAN GLUN1/GLUN2A LBD IN COMPLEX WITH COMPOUND 9 (GNE3500)
 
Authors :  H. J. A. Wallweber, P. J. Lupardus
Date :  20 Oct 16  (Deposition) - 30 Nov 16  (Release) - 01 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.48
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nmda Receptor, Glutamate, Glycine, Calcium Channel, Membrane, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Villemure, M. Volgraf, Y. Jiang, G. Wu, C. Q. Ly, P. W. Yuen, A. Lu, X. Luo, M. Liu, S. Zhang, P. J. Lupardus, H. J. Wallweber, B. M. Liederer G. Deshmukh, E. Plise, S. Tay, T. M. Wang, J. E. Hanson, D. H. Hackos, K. Scearce-Levie, J. B. Schwarz, B. D. Sellers
Glun2A-Selective Pyridopyrimidinone Series Of Nmdar Positiv Allosteric Modulators With An Improved In Vivo Profile.
Acs Med Chem Lett V. 8 84 2017
PubMed-ID: 28105280  |  Reference-DOI: 10.1021/ACSMEDCHEMLETT.6B00388

(-) Compounds

Molecule 1 - GLUTAMATE RECEPTOR IONOTROPIC, NMDA 2A
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    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: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    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  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
17H21Ligand/Ion(1R,2R)-2-(2-{[5-CHLORO-3-(TRIFLUOROMETHYL)-1H-PYRAZOL-1-YL]METHYL}-7-METHYL-4-OXO-4H-PYRIDO[1,2-A]PYRIMIDIN-6-YL)CYCLOPROPANE-1-CARBONITRILE
2GLU1Mod. Amino AcidGLUTAMIC ACID
3GLY1Mod. Amino AcidGLYCINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS 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:408 , HOH A:416 , HOH A:428binding site for residue GLU A 301
2AC2SOFTWAREILE A:116 , PRO A:129 , PHE A:130 , VAL A:131 , GLU A:132 , THR A:242 , GLY A:243 , VAL A:266 , ILE B:128 , LYS B:140 , PRO B:141 , TYR B:144 , LEU B:270 , HIS B:273binding site for residue 7H2 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:225binding site for residue GLY B 301

(-) SS Bonds  (6, 6)

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
6B:237 -B:291

(-) 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 5TPA)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5TPA)

(-) 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:276
                                                                                                                                                                                                                                                                                                                    
               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....eeeeehhhhhhhhhhhhhh.eeehhhhh.eeeeee..ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5tpa A   6 NHLSIVTLEEAPFVIVEDIDETCVRNTVPCRKFVKINNSTNEGMNVKKCCKGFCIDILKKLSRTVKFTYDLYLVTNGKHGKKVNNVWNGMIGEVVYQRAVMAVGSLTINEERSEVVDFSVPFVETGISVMVSRGTQVTGLSDKKFQRPHDYSPPFRFGTVPNGSTERNIRNNYPYMHQYMTKFNQKGVEDALVSLKTGKLDAFIYDAAVLNYKAGRDEGCKLVTIGSGYIFATTGYGIALQKGSPWKRQIDLALLQFVGDGEMEELETLWLTGICE 301
                                    15        25|       38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278    ||
                                              25|                                                                                                                                                                                                                                                           283|
                                               29                                                                                                                                                                                                                                                            301


Chain B from PDB  Type:PROTEIN  Length:280
                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.......eeee.................eeeeee..........eeeeeeehhhhhhhhhhhhhhh..eeeee........ee....eehhhhhhhhh....ee......hhhhhh.eee....eeeeeeeeee.........hhhhhh......ee....hhhhhhhhhh..hhhhhhhhh.....hhhhhhhhhhh....eeeeehhhhhhhhhhh..eeeeeeeeeeeee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tpa B   3 MSTRLKIVTIHQEPFVYVKPTLSDGTCKEEFTDPVKKVICTGPNDTSPGSPRHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKGTRITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRCG 301
                                    12        22        32 ||     45        55        65        75        85        95   ||  109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       301
                                                          34|                                                           99|                                                                                                                                                                                    287||
                                                           38                                                           104                                                                                                                                                                                     291|
                                                                                                                                                                                                                                                                                                                 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 5TPA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 5h8h 5h8n 5h8q 5i2k 5i2n 5kcj 5kdt 5tp9
        NMDZ1_HUMAN | Q05586: 2hqw 2nr1 3bya 5h8f 5h8h 5h8n 5h8q 5i2k 5i2n 5kcj 5kdt 5tp9

(-) Related Entries Specified in the PDB File

5tp9