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(-) Description

Title :  CRYSTAL STRUCTURE OF AMINO TERMINAL DOMAINS OF THE NMDA RECEPTOR SUBUNIT GLUN1 AND GLUN2B IN COMPLEX WITH IFENPRODIL
 
Authors :  J. Pandit
Date :  20 Nov 15  (Deposition) - 02 Mar 16  (Release) - 13 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.77
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Glutamate Receptor, Allosteric Modulator, Glun2B Antagonists, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Stroebel, D. L. Buhl, J. D. Knafels, P. K. Chanda, M. Green, S. Sciabola, L. Mony, P. Paoletti, J. Pandit
A Novel Binding Mode Reveals Two Distinct Classes Of Nmda Receptor Glun2B-Selective Antagonists.
Mol. Pharmacol. V. 89 541 2016
PubMed-ID: 26912815  |  Reference-DOI: 10.1124/MOL.115.103036

(-) Compounds

Molecule 1 - NMDA GLUTAMATE RECEPTOR SUBUNIT
    Chains: A, C
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: AMINO TERMINAL DOMAIN (UNP RESIDUES 23-408)
    Gene: GRIN1, NR1
    Mutation: YES
    Organism Common: AFRICAN CLAWED FROG
    Organism Scientific: XENOPUS LAEVIS
    Organism Taxid: 8355
 
Molecule 2 - GLUTAMATE RECEPTOR IONOTROPIC, NMDA 2B
    Chains: B, D
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: AMINO TERMINAL DOMAIN (UNP RESIDUES 31-394)
    Gene: GRIN2B, NMDAR2B
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GLUN2B,GLUTAMATE [NMDA] RECEPTOR SUBUNIT EPSILON-2,N-METHYL D-ASPARTATE RECEPTOR SUBTYPE 2B,NR2B,N-METHYL-D-ASPARTATE RECEPTOR SUBUNIT 3,HNR3

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 15)

Asymmetric Unit (5, 15)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2MAN2Ligand/IonALPHA-D-MANNOSE
3NA2Ligand/IonSODIUM ION
4NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
5QEL2Ligand/Ion4-[(1R,2S)-2-(4-BENZYLPIPERIDIN-1-YL)-1-HYDROXYPROPYL]PHENOL
Biological Unit 1 (4, 9)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2MAN2Ligand/IonALPHA-D-MANNOSE
3NA-1Ligand/IonSODIUM ION
4NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
5QEL1Ligand/Ion4-[(1R,2S)-2-(4-BENZYLPIPERIDIN-1-YL)-1-HYDROXYPROPYL]PHENOL
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1BMA-1Ligand/IonBETA-D-MANNOSE
2MAN-1Ligand/IonALPHA-D-MANNOSE
3NA-1Ligand/IonSODIUM ION
4NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
5QEL1Ligand/Ion4-[(1R,2S)-2-(4-BENZYLPIPERIDIN-1-YL)-1-HYDROXYPROPYL]PHENOL

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:137 , ASP A:364 , HOH A:604 , HOH A:628binding site for residue NA A 501
02AC2SOFTWARETYR A:109 , THR A:110 , SER A:132 , LEU A:135 , GLN B:110 , PHE B:176 , PRO B:177 , GLU B:236 , HOH B:610binding site for residue QEL B 503
03AC3SOFTWAREHIS C:134 , PHE C:137 , ASP C:364 , HOH C:612binding site for residue NA C 501
04AC4SOFTWARETYR C:109 , SER C:132 , ILE C:133 , GLN D:110 , ILE D:111 , PHE D:176 , PRO D:177 , GLU D:236binding site for residue QEL D 503
05AC5SOFTWAREASN A:297 , SER A:299 , ALA A:300 , HOH A:656binding site for Mono-Saccharide NAG A 502 bound to ASN A 297
06AC6SOFTWAREGLN A:40 , ILE A:41 , GLU A:44 , GLN A:48 , LYS A:51 , ASN A:389 , TYR A:392 , HOH A:642 , HOH A:648 , HOH A:656 , HOH A:659binding site for Poly-Saccharide residues NAG A 503 through MAN A 507 bound to ASN A 389
07AC7SOFTWAREASN B:74binding site for Mono-Saccharide NAG B 501 bound to ASN B 74
08AC8SOFTWAREASN B:341 , HOH B:628binding site for Mono-Saccharide NAG B 502 bound to ASN B 341
09AC9SOFTWAREASN C:294 , ASN C:297 , SER C:299 , ALA C:300 , VAL C:355 , HOH C:605binding site for Mono-Saccharide NAG C 502 bound to ASN C 297
10AD1SOFTWAREASN D:74binding site for Mono-Saccharide NAG D 501 bound to ASN D 74
11AD2SOFTWAREASN D:341 , THR D:343binding site for Mono-Saccharide NAG D 502 bound to ASN D 341

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:79 -A:329
2B:86 -B:321
3C:79 -C:329
4D:86 -D:321

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5EWJ)

(-) Sequences/Alignments

Asymmetric 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:357
                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee.hhhhhhhhhhhhhhhhhhh....eeeeeeeee...hhhhhhhhhhhhhhhh.eeeeee......hhhhhhhhhhh...eee....hhhhhh......eee...hhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhh..eeeeeeee......hhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhh.......eee..hhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhh..eeee..eeeee.....ee...eeeeeee..eeeeeeee....eee............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ewj A  23 DPKIVNIGAVLSTKKHEQIFREAVNQANKRHFTRKIQLQATSVTHRPNAIQMALSVCEDLISSQVYAILVSHPPLTPTPISYTAGFYRIPVIGLTTRMSIYSDKSIHLSFLRTVPPYSHQALVWFEMMRLFNWNHVILIVSDDHEGRAAQKKLETLLEGPKADKVLQFEPGTKNLTALLLEAKELEARVIILSASEDDATAVYKSAAMLDMTGAGYVWLVGEREISGSALRYAPDGIIGLQLINGKNESAHISDAVAVVAQAIHELFEMENITDPPRGCVGNTNIWKTGPLFKRVLMSSKYPDGVTGRIEFNEDGDRKFAQYSIMNLQNRKLVQVGIFNGSYIIQNDRKIIWPGGET 407
                                    32        42        52        62        72        82        92   ||  107       117       127       137       147       157       167       177       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       
                                                                                                    96|                                                                                185|                                                                                                                                                                                                      
                                                                                                    102                                                                                 209                                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:353
                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee...hhhhhh....eeeeeeeee...hhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhhhhhhhhh..eeeeehhhhh..........eee...hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhh.....eeeeeee.........hhhhhhhh.....eeeee.hhhhhhhhhhhhhhh.......eeeeehhhhh.............eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh......................hhhhhh..ee..ee.............eeeeee.....eeeeeee....eee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ewj B  32 PPSIGIAVILVGTSDEVAIKDLSVVPRVELVAMNETDPKSIITRICDLMSDRKIQGVVFADDTDQEAIAQILDFISAQTLTPILGIHGGSSMIMADKDESSMFFQFGPSIEQQASVMLNIMEEYDWYIFSIVTTYFPGYQDFVNKIRSTIENSFVGWELEEVLLLDMSLDDGDSKIQNQLKKLQSPIILLYCTKEEATYIFEVANSVGLTGYGYTWIVPSLVAGDTDTVPAEFPTGLISVSYDEWDYGLPARVRDGIAIITTAASDMLSEHSFIPEPKSSCYNTHEKRIYQSNMLNRYLINVTFEGRDLSFSEDGYQMHPKLVIILLNKERKWERVGKWKDKSLQMKYYVWPR 393
                                    41        51||      70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390   
                                               52|                                                                                                                                                                                                                                                                                                                                           
                                                62                                                                                                                                                                                                                                                                                                                                           


Chain C from PDB  Type:PROTEIN  Length:356
                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee.hhhhhhhhhhhhhhhhhhhh...eeeeeeeee...hhhhhhhhhhhhhhhh.eeeeee.....hhhhhhhhhhh...eee....hhhhhh......eee...hhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhh..eeeeeeee......hhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhh.......eee..hhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhh..eeee..eeeee.....ee...eeeeeee..eeeeeeee....eee............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ewj C  23 DPKIVNIGAVLSTKKHEQIFREAVNQANKRHFTRKIQLQATSVTHRPNAIQMALSVCEDLISSQVYAILVSHPLTPTPISYTAGFYRIPVIGLTTRMSIYSDKSIHLSFLRTVPPYSHQALVWFEMMRLFNWNHVILIVSDDHEGRAAQKKLETLLEGPKADKVLQFEPGTKNLTALLLEAKELEARVIILSASEDDATAVYKSAAMLDMTGAGYVWLVGEREISGSALRYAPDGIIGLQLINGKNESAHISDAVAVVAQAIHELFEMENITDPPRGCVGNTNIWKTGPLFKRVLMSSKYPDGVTGRIEFNEDGDRKFAQYSIMNLQNRKLVQVGIFNGSYIIQNDRKIIWPGGET 407
                                    32        42        52        62        72        82        92  ||   108       118       128       138       148       158       168       178      |211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401      
                                                                                                   95|                                                                                185|                                                                                                                                                                                                      
                                                                                                   102                                                                                 209                                                                                                                                                                                                      


Chain D from PDB  Type:PROTEIN  Length:355
                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee...hhhhhh.......eeeeeeeee...hhhhhhhhhhhhhhhh.eeeeeeee....hhhhhhhhhhhhhhh..eeeeehhhhh..........eee...hhhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhhhh.....eeeeeeee........hhhhhhhh.....eeeee.hhhhhhhhhhhhhhh.......eeeehhhhhh.............eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhh.......hhhhhh...................eeeeee.....eeeeeee....eee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ewj D  32 PPSIGIAVILVGTSDEVAIKDFHHLSVVPRVELVAMNETDPKSIITRICDLMSDRKIQGVVFADDTDQEAIAQILDFISAQTLTPILGIHGGSSMIMADKDESSMFFQFGPSIEQQASVMLNIMEEYDWYIFSIVTTYFPGYQDFVNKIRSTIENSFVGWELEEVLLLDMSLDDGDSKIQNQLKKLQSPIILLYCTKEEATYIFEVANSVGLTGYGYTWIVPSLVAGDTDTVPAEFPTGLISVSYDEWDYGLPARVRDGIAIITTAASDMLSEHSFIPEPKSSCYNTHEKRIYQSNMLNRYLINVTFEDLSFSEDGYQMHPKLVIILLNKERKWERVGKWKDKSLQMKYYVWPRM 394
                                    41        51||      67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       349       359       369       379       389     
                                               52|                                                                                                                                                                                                                                                                                           345|                                              
                                                59                                                                                                                                                                                                                                                                                            348
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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 5EWJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (32, 46)

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 Related Entries

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

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        NMDE2_HUMAN | Q13224: 1s11 1s2s 2ipv 5ewl 5ewm
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        Q91977_XENLA | Q91977: 3qek 3qel 3qem 5b3j 5ewl 5ewm 5tpw 5tpz 5tq0 5tq2

(-) Related Entries Specified in the PDB File

5ewl 5ewm