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(-) Description

Title :  GLUTAMATE- AND DCKA-BOUND GLUN1/GLUN2A AGONIST BINDING DOMAINS WITH MPX-007
 
Authors :  T. -C. Mou, S. R. Sprang, K. B. Hansen
Date :  10 May 16  (Deposition) - 21 Sep 16  (Release) - 05 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.72
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
    Fragment: UNP RESIDUES 415-565;
684-821
    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
    Fragment: UNP RESIDUES 402-539;
661-800
    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
12JK1Ligand/Ion4-HYDROXY-5,7-DIMETHYLQUINOLINE-2-CARBOXYLIC ACID
26ND1Ligand/Ion5-({[(3,4-DIFLUOROPHENYL)SULFONYL]AMINO}METHYL)-6-METHYL-N-[(2-METHYL-1,3-THIAZOL-5-YL)METHYL]PYRAZINE-2-CARBOXAMIDE
3GLU1Mod. Amino AcidGLUTAMIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:13 , PHE A:16 , PHE A:92 , PRO A:124 , LEU A:125 , THR A:126 , ARG A:131 , TRP A:223 , VAL A:227 , PHE A:250binding site for residue 2JK A 501
2AC2SOFTWAREPRO A:140 , ARG A:247 , SER A:248 , GLY A:249 , 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 , LEU B:280binding site for residue 6ND B 601
3AC3SOFTWAREHIS 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:705binding site for residue GLU B 602

(-) 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
3Leu B:28 -Thr B:29
4Ser B:161 -Pro B:162

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5JTY)

(-) 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:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.......eeee....................eeeee...eeeeeehhhhhhhhhhhhhh...eeeee........ee..eehhhhhhhhhh...ee......hhhhhh.eee....eeeeeeeee........hhhhhh......ee....hhhhhhhhhh..hhhhhhhhhh....hhhhhhhhhhh....eeeeehhhhhhhhh.eeeeeeeeeeee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jty A   4 TRLKIVTIHQEPFVYVKPTMSDGTCKEEFTVNGDPVKKVICTGPHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQEKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKTRITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVR 286
                                    13        23        33        43   ||   62        72        82        92   ||  108       118       128       138       148  ||   160       170       180       190       200       210       220       230  ||   244       254       264       274       284  
                                                                      47|                                     96|                                             151|                                                                            233|                                                
                                                                       57                                     103                                              154                                                                             238                                                


Chain B from PDB  Type:PROTEIN  Length:276
                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.......eee.............eeeeeeee.......eeeeeeeeehhhhhhhhhhhhhh..eeeeee........ee..eehhhhhhhhh....ee......hhhhhh..ee....eeeeeeeeee.........hhhhhhhhhh.....ee....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh....eeeeehhhhhhhhhh.....eee...eeeeee..ee....hhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5jty B   6 DNHLSIVTLEEAPFVIVEDIDPLTETCVRNTVPCRKFVKINNSTNEGMNVKKCCKGFCIDILKKLSRTVKFTYDLYLVTNGKHGKKVNNVWNGMIGEVVYQRAVMAVGSLTINEERSEVVDFSVPFVETGISVMVSRGTQVTGLSDKKFQRPHDYSPPFRFGTVPNGSTERNIRNNYPYMHQYMTRFNQRGVEDALVSLKTGKLDAFIYDAAVLNYKAGRDEGCKLVTIGIFATTGYGIALQKGSPWKRQIDLALLQFVGDGEMEELETLWLTGIC 284
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235|      248       258       268       278      
                                                                                                                                                                                                                                                               235|                                             
                                                                                                                                                                                                                                                                239
   Legend:   → Mismatch (orange background)
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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 5JTY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 ]  
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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 5i58 5i59 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 5i58 5i59 5u8c 5vih 5vii 5vij

(-) Related Entries Specified in the PDB File

5i57 5i58 5i59