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(-) Description

Title :  GLUTAMATE- AND GLYCINE-BOUND GLUN1/GLUN2A AGONIST BINDING DOMAINS WITH MPX-004
 
Authors :  T. -C. Mou, S. R. Sprang, K. B. Hansen
Date :  14 Feb 16  (Deposition) - 21 Sep 16  (Release) - 05 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.52
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nmda Receptor, Antagonist, Transport Protein, Receptor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Yi, T. C. Mou, K. N. Dorsett, R. A. Volkmann, F. S. Menniti, S. R. Sprang, K. B. Hansen
Structural Basis For Negative Allosteric Modulation Of Glun2A-Containing Nmda Receptors.
Neuron V. 91 1316 2016
PubMed-ID: 27618671  |  Reference-DOI: 10.1016/J.NEURON.2016.08.014

(-) Compounds

Molecule 1 - GLUTAMATE RECEPTOR IONOTROPIC, NMDA 1,GLUTAMATE RECEPTOR IONOTROPIC, NMDA 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: GRIN1, NMDAR1
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: GLUN1,GLUTAMATE [NMDA] RECEPTOR SUBUNIT ZETA-1,N-METHYL-D- ASPARTATE RECEPTOR SUBUNIT NR1,NMD-R1,GLUN1,GLUTAMATE [NMDA] RECEPTOR SUBUNIT ZETA-1,N-METHYL-D-ASPARTATE RECEPTOR SUBUNIT NR1,NMD-R1
 
Molecule 2 - GLUTAMATE RECEPTOR IONOTROPIC, NMDA 2A,GLUTAMATE RECEPTOR IONOTROPIC, NMDA 2A
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: GRIN2A
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: GLUN2A,GLUTAMATE [NMDA] RECEPTOR SUBUNIT EPSILON-1,N-METHYL D-ASPARTATE RECEPTOR SUBTYPE 2A,NR2A,GLUN2A,GLUTAMATE [NMDA] RECEPTOR SUBUNIT EPSILON-1,N-METHYL D-ASPARTATE RECEPTOR SUBTYPE 2A,NR2A

 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
167R1Ligand/Ion5-({[(3-CHLORO-4-FLUOROPHENYL)SULFONYL]AMINO}METHYL)-N-[(2-METHYL-1,3-THIAZOL-5-YL)METHYL]PYRAZINE-2-CARBOXAMIDE
2GLU1Mod. Amino AcidGLUTAMIC ACID
3GLY1Mod. Amino AcidGLYCINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:92 , PRO A:124 , LEU A:125 , THR A:126 , ARG A:131 , SER A:180 , TRP A:223 , ASP A:224 , PHE A:250binding site for residue GLY A 1001
2AC2SOFTWAREHIS B:88 , SER B:114 , LEU B:115 , THR B:116 , ARG B:121 , GLY B:172 , SER B:173 , THR B:174 , TYR B:214 , ASP B:215 , HOH B:522binding site for residue GLU B 301
3AC3SOFTWAREILE A:127 , PRO A:140 , ARG A:247 , SER A:248 , GLY A:249 , HOH A:1101 , HOH A:1111 , VAL B:129 , PRO B:130 , PHE B:131 , VAL B:132 , GLU B:133 , LEU B:264 , VAL B:267 , MET B:272 , GLU B:276 , HOH B:532binding site for residue 67R B 302

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:28 -A:62
2A:44 -A:63
3B:32 -B:58
4B:39 -B:59
5B:229 -B:284

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Glu A:14 -Pro A:15
2Ala B:17 -Pro B:18
3Ser B:141 -Arg B:142
4Ser B:161 -Pro B:162

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5I58)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5I58)

(-) Exons   (0, 0)

(no "Exon" information available for 5I58)

(-) 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:258
                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee.......eeee..........eeee...eeeeehhhhhhhhhhhhhh...eeeee........ee...eehhhhhhhhhh...ee......hhhhhhhhee....eeeeeeeeee.........hhhhhh......ee....hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh....eeeeehhhhhhhhh....eeeeeeeeeeeee..ee.....hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5i58 A    3 STRLKIVTIHQEPFVYVKPTMSDGTCVKKVICTGPVPQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKGTRITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVG 1001
                                    12        22     || 42    ||  63        73        83        93    || 108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278      ||
                                                    28|      47|                                     98|                                                                                                                                                                                  285|
                                                     39       59                                     104                                                                                                                                                                                  1001


Chain B from PDB  Type:PROTEIN  Length:278
                                                                                                                                                                                                                                                                                                                       
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......eee...........eeeeeeee.......eeeeeeeeehhhhhhhhhhhhhh..eeeeee..............hhhhhhhhh....eee.....hhhhhh..ee....eeeeeeeee..........hhhhhhhhhh.....ee....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh....eeeeehhhhhhhhhh......ee.hhh..eeeeee..ee.....hhhhhhhhhhhhhhh.hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5i58 B    6 DNHLSIVTLEEAPFVIVEDIDPETCVRNTVPCRKFVKINNSTNEGMNVKKCCKGFCIDILKKLSRTVKFTYDLYLVTNGKHGKKVNNVWNGMIGEVVYQRAVMAVGSLTINEERSEVVDFSVPFVETGISVMVSRGTQVTGLSDKKFQRPHDYSPPFRFGTVPNGSTERNIRNNYPYMHQYMTRFNQRGVEDALVSLKTGKLDAFIYDAAVLNYKAGRDEGCKLVTIGSGYIFATTGYGIALQKGSPWKRQIDLALLQFVGDGEMEELETLWLTGICE  301
                                    15        25 ||     37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277      ||
                                                27|                                                                                                                                                                                                                                                           284|
                                                 30                                                                                                                                                                                                                                                            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 5I58)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5I58)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5I58)

(-) Gene Ontology  (79, 116)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala B:17 - Pro B:18   [ RasMol ]  
    Glu A:14 - Pro A:15   [ RasMol ]  
    Ser B:141 - Arg B:142   [ RasMol ]  
    Ser B:161 - Pro B:162   [ RasMol ]  
 

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  5i58
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  NMDE1_RAT | Q00959
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  NMDZ1_RAT | P35439
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 Related Entries

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

UniProtKB/Swiss-Prot
        NMDE1_RAT | Q00959: 2a5s 2a5t 4jwx 4nf4 4nf5 4nf6 4nf8 5ddn 5ddx 5de4 5dex 5i56 5i57 5i59 5jty 5tpw 5tq0 5tq2 5vih 5vii 5vij
        NMDZ1_RAT | P35439: 1pb7 1pb8 1pb9 1pbq 1y1m 1y1z 1y20 2a5t 3q41 4kcc 4kfq 4nf4 4nf5 4nf6 4nf8 4pe5 5ddn 5ddx 5de4 5dex 5fxg 5fxh 5fxi 5fxj 5fxk 5i56 5i57 5i59 5jty 5u8c 5vih 5vii 5vij

(-) Related Entries Specified in the PDB File

5i56 5i57 5i58