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(-) Description

Title :  CRYSTAL STRUCTURE OF AMINO TERMINAL DOMAINS OF THE NMDA RECEPTOR SUBUNIT GLUN1 AND GLUN2B IN COMPLEX WITH EVT-101
 
Authors :  J. Pandit
Date :  20 Nov 15  (Deposition) - 02 Mar 16  (Release) - 13 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.76
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, 18)

Asymmetric Unit (5, 18)
No.NameCountTypeFull Name
15SM2Ligand/Ion5-[3-[BIS(FLUORANYL)METHYL]-4-FLUORANYL-PHENYL]-3-[(2-METHYLIMIDAZOL-1-YL)METHYL]PYRIDAZINE
2BMA1Ligand/IonBETA-D-MANNOSE
3MAN2Ligand/IonALPHA-D-MANNOSE
4NA5Ligand/IonSODIUM ION
5NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (4, 9)
No.NameCountTypeFull Name
15SM1Ligand/Ion5-[3-[BIS(FLUORANYL)METHYL]-4-FLUORANYL-PHENYL]-3-[(2-METHYLIMIDAZOL-1-YL)METHYL]PYRIDAZINE
2BMA1Ligand/IonBETA-D-MANNOSE
3MAN2Ligand/IonALPHA-D-MANNOSE
4NA-1Ligand/IonSODIUM ION
5NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
15SM1Ligand/Ion5-[3-[BIS(FLUORANYL)METHYL]-4-FLUORANYL-PHENYL]-3-[(2-METHYLIMIDAZOL-1-YL)METHYL]PYRIDAZINE
2BMA-1Ligand/IonBETA-D-MANNOSE
3MAN-1Ligand/IonALPHA-D-MANNOSE
4NA-1Ligand/IonSODIUM ION
5NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:137 , ASP A:364 , HOH A:635 , HOH A:671binding site for residue NA A 501
02AC2SOFTWAREVAL A:385 , ASN A:396 , ARG A:398binding site for residue NA A 508
03AC3SOFTWAREASN A:50 , LYS A:51 , HIS A:53 , THR A:55 , GLN A:395 , HOH A:641binding site for residue NA A 509
04AC4SOFTWARETYR A:109 , THR A:110 , ILE A:133 , PRO B:78 , GLN B:110 , ILE B:111 , PHE B:114 , MET B:134 , ALA B:135 , ASP B:136 , PRO B:177 , HOH B:621binding site for residue 5SM B 503
05AC5SOFTWAREARG B:328 , GLN B:331 , SER D:312binding site for residue NA B 504
06AC6SOFTWARETYR C:128 , PHE C:137 , ASP C:364 , ASP C:366binding site for residue NA C 501
07AC7SOFTWARETYR C:109 , THR C:110 , PHE C:113 , ILE C:133 , PRO D:78 , ILE D:82 , GLN D:110 , ILE D:111 , PHE D:114 , ALA D:135 , ASP D:136 , PRO D:177binding site for residue 5SM D 503
08AC8SOFTWAREASN A:297 , ALA A:300 , VAL A:355binding site for Mono-Saccharide NAG A 502 bound to ASN A 297
09AC9SOFTWAREGLN A:40 , ILE A:41 , GLU A:44 , ALA A:45 , GLN A:48 , LYS A:51 , ASN A:389 , HOH A:637 , HOH A:638binding site for Poly-Saccharide residues NAG A 503 through MAN A 507 bound to ASN A 389
10AD1SOFTWAREASN B:74binding site for Mono-Saccharide NAG B 501 bound to ASN B 74
11AD2SOFTWAREASN B:341 , THR B:343binding site for Mono-Saccharide NAG B 502 bound to ASN B 341
12AD3SOFTWAREASN 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
13AD4SOFTWAREASN D:74binding site for Mono-Saccharide NAG D 501 bound to ASN D 74
14AD5SOFTWAREASN 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 5EWM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5EWM)

(-) 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
                 5ewm 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:356
                                                                                                                                                                                                                                                                                                                                                                                                    
               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.........hhhhhhhhh....eeeee.hhhhhhhhhhhhhhh.......eeeehhhhhh.............eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhh...hhhhhh..ee..ee.............eeeeee.....eeeeeee....eee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ewm B  32 PPSIGIAVILVGTSDEVAIKDFHHLSVVPRVELVAMNETDPKSIITRICDLMSDRKIQGVVFADDTDQEAIAQILDFISAQTLTPILGIHGGSSMIMADKDESSMFFQFGPSIEQQASVMLNIMEEYDWYIFSIVTTYFPGYQDFVNKIRSTIENSFVGWELEEVLLLDMSLDDGDSKIQNQLKKLQSPIILLYCTKEEATYIFEVANSVGLTGYGYTWIVPSLVAGDTDTVPAEFPTGLISVSYDEWDYGLPARVRDGIAIITTAASDMLSEHSFIPEPKSSCYNTHEKRIYQSNMLNRYLINVTFEGRDLSFSEDGYQMHPKLVIILLNKERKWERVGKWKDKSLQMKYYVWPR 393
                                    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       347       357       367       377       387      
                                               52|                                                                                                                                                                                                                                                                                                                                              
                                                59                                                                                                                                                                                                                                                                                                                                              


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
                 5ewm 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...hhhhhhh......eeeeeeeee...hhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhhhhhhhhh..eeeeehhhh...........eee...hhhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhhhh.....eeeeeeee........hhhhhhhh.....eeeee.hhhhhhhhhhhhhhh.......eeeehhhhhh.............eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhh...hhhhhh...................eeeeee.....eeeeeee....eee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ewm 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 5EWM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 5ewj 5ewl
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        Q91977_XENLA | Q91977: 3qek 3qel 3qem 5b3j 5ewj 5ewl 5tpw 5tpz 5tq0 5tq2

(-) Related Entries Specified in the PDB File

5wmj 5wml