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(-) Description

Title :  CRYSTAL STRUCTURE OF AMINO TERMINAL DOMAINS OF THE NMDA RECEPTOR SUBUNIT GLUN1 AND GLUN2B IN APO CLOSED STATE
 
Authors :  A. Romero-Hernandez, N. Simorwski, E. Karakas, H. Furukawa
Date :  21 Oct 16  (Deposition) - 14 Dec 16  (Release) - 14 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,D
Keywords :  Ion Channel, Nmda Receptor, Allosteric Modulation, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Romero-Hernandez, N. Simorowski, E. Karakas, H. Furukawa
Molecular Basis For Subtype Specificity And High-Affinity Zinc Inhibition In The Glun1-Glun2A Nmda Receptor Amino-Terminal Domain
Neuron V. 92 1 2016
PubMed: search  |  Reference-DOI: 10.1016/J.NEURON.2016.11.006

(-) Compounds

Molecule 1 - NMDA GLUTAMATE RECEPTOR SUBUNIT
    ChainsA
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System CommonCABBAGE LOOPER
    Expression System Taxid7111
    FragmentRESIDUES 23-405
    GeneGRIN1, NR1
    Organism CommonAFRICAN CLAWED FROG
    Organism ScientificXENOPUS LAEVIS
    Organism Taxid8355
 
Molecule 2 - GLUTAMATE RECEPTOR IONOTROPIC, NMDA 2B
    ChainsD
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System CommonCABBAGE LOOPER
    Expression System Taxid7111
    FragmentRESIDUES 32-393
    GeneGRIN2B
    Organism CommonRAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymGLUN2B,GLUTAMATE [NMDA] RECEPTOR SUBUNIT EPSILON-2,N-METHYL D-ASPARTATE RECEPTOR SUBTYPE 2B,NR2B

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:224 , THR A:226 , MET A:258binding site for Mono-Saccharide NAG A 501 bound to ASN A 224
2AC2SOFTWAREASN A:294 , ASN A:297 , SER A:299binding site for Mono-Saccharide NAG A 502 bound to ASN A 297
3AC3SOFTWAREASN A:321binding site for Mono-Saccharide NAG A 503 bound to ASN A 321
4AC4SOFTWAREASN D:341 , THR D:343 , ASP D:348 , SER D:350binding site for Mono-Saccharide NAG D 401 bound to ASN D 341

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:79 -A:329
2D:86 -D:321

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5TPZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5TPZ)

(-) 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:354
                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeee.hhhhhhhhhhhhhhhhhhh....eeeee..ee...hhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhh..eee....hhhhhh......eee...hhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhh.....eeeeee......hhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh........eee..hhhhh..hhhhh...eeeeee....hhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhh......................eeeeeee..eeeeeeee....eee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5tpz A  23 DPKIVNIGAVLSTKKHEQIFREAVNQANKRHFTRKIQLQATSVTHRPNAIQMALSVCEDLISSQVYAILVSHLTPTPISYTAGFYRIPVIGLTTRMSIYSDKSIHLSFLRTVPPYSHQALVWFEMMRLFNWNHVILIVSDDHEGRAAQKKLETLLEGKPKADKVLQFEPGTKNLTALLLEAKELEARVIILSASEDDATAVYKSAAMLDMTGAGYVWLVGEREISGSALRYAPDGIIGLQLINGKNESAHISDAVAVVAQAIHELFEMENITDPPRGCVGNTNIWKTGPLFKRVLMSSKYPDGVTGRIEFNEDGDRKFAQYSIMNLQNRKLVQVGIFNGSYIIQNDRKIIWPGG 405
                                    32        42        52        62        72        82        92||     109       119       129       139       149       159       169       179       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401    
                                                                                                 93|                                                                                   187|                                                                                                                                                                                                   
                                                                                                 101                                                                                    210                                                                                                                                                                                                   

Chain D from PDB  Type:PROTEIN  Length:352
                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee............eeeeeeeee...hhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhhh..eeeeehhhhh..........eee...hhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhh.....eeeeeee.........hhhhhhhh.....eeeee.hhhhhhhhhhhhhhh.......eee.hhhhhh..............eeee.....hhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhh.....................eeeeee.....eeeeeee....eee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tpz D  32 PPSIGIAVILVGTSDEVFHHLSVVPRVELVAMNETDPKSIITRICDLMSDRKIQGVVFADDTDQEAIAQILDFISAQTLTPILGIHGGSSMIMADKDESSMFFQFGPSIEQQASVMLNIMEEYDWYIFSIVTTYFPGYQDFVNKIRSTIENSFVGWELEEVLLLDMSLDDGDSKIQNQLKKLQSPIILLYCTKEEATYIFEVANSVGLTGYGYTWIVPSLVAGDTDTVPSEFPTGLISVSYDEWDYGLPARVRDGIAIITTAASDMLSEHSFIPEPKSSCYNTHEKRIYQSNMLNRYLINVTFEGRDLSFSEDGYQMHPKLVIILLNKERKWERVGKWKDKSLQMKYYVWPR 393
                                    41      ||61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391  
                                           48|                                                                                                                                                                                                                                                                                                                                              
                                            59                                                                                                                                                                                                                                                                                                                                              

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  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 5TPZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (74, 88)

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
        NMDE2_RAT | Q009603jpw 3jpy 3qel 3qem 4pe5 5b3j 5fxg 5fxh 5fxi 5fxj 5fxk
UniProtKB/TrEMBL
        Q91977_XENLA | Q919773qek 3qel 3qem 5b3j 5ewj 5ewl 5ewm 5tpw 5tq0 5tq2

(-) Related Entries Specified in the PDB File

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