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(-) Description

Title :  AGONIST-BOUND GLUN1/GLUN2A AGONIST BINDING DOMAINS WITH TCN201
 
Authors :  T. -C. Mou, S. R. Sprang, K. B. Hansen
Date :  14 Feb 16  (Deposition) - 07 Sep 16  (Release) - 05 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.28
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
(for further references see the PDB file header)

(-) 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
167P1Ligand/IonN-({4-[2-(BENZENECARBONYL)HYDRAZINECARBONYL]PHENYL}METHYL)-3-CHLORO-4-FLUOROBENZENE-1-SULFONAMIDE
2GLU1Mod. Amino AcidGLUTAMIC ACID
3GLY1Mod. Amino AcidGLYCINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:92 , PRO A:124 , THR A:126 , ARG A:131 , SER A:296 , ASP A:340binding site for residue GLY A 501
2AC2SOFTWAREHIS B:88 , SER B:114 , THR B:116 , ARG B:121 , GLY B:172 , SER B:173 , THR B:174 , TYR B:214 , ASP B:215 , HOH B:914 , HOH B:919binding site for residue GLU B 801
3AC3SOFTWAREILE A:127 , PRO A:140 , TYR A:143 , ARG A:363 , SER A:364 , GLY A:365 , 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:280 , HOH B:903 , HOH B:904 , HOH B:938binding site for residue 67P B 802

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:28 -A:62
2A:44 -A:63
3A:352 -A:406
4B:32 -B:58
5B:39 -B:59
6B:229 -B:284

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Glu A:14 -Pro A:15
2Val A:98 -Asn A:99
3Glu A:405 -Cys A:406
4Ala B:17 -Pro B:18
5Ser B:161 -Pro B:162
6Gly B:235 -Ser B:236

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5I56)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5I56)

(-) Exons   (0, 0)

(no "Exon" information available for 5I56)

(-) 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:287
                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.......eeee....................eeeeee..........eeeeeeehhhhhhhhhhhhhh...eeeee........eee....eeehhhhhhhhhh...ee......hhhhhh..ee....eeeeeeeeee.........hhhhhh......ee....hhhhhhhhhh..hhhhhhhhh.....hhhhhhhhhhh....eeeeehhhhhhhhhhh..eeeeeeeeeeeee..ee.....hhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i56 A   4 TRLKIVTIHQEPFVYVKPTMSDGTCKEEFTVNGDPVKKVICTGPNDTSPGSPRHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKGTRITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQECDG 501
                                    13        23        33        43        53        63        73        83        93     ||105       115       125       135       145      |271       281       291       301       311       321       331       341       351       361       371       381       391       401     ||
                                                                                                                          99|                                               152|                                                                                                                                       407|
                                                                                                                          102                                                269                                                                                                                                        501


Chain B from PDB  Type:PROTEIN  Length:281
                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.......eeee............eeeeeeee.......eeeeeeeeehhhhhhhhhhhhhh..eeeeee........ee..eehhhhhhhhh....ee......hhhhhh..ee....eeeeeeeeee.........hhhhhhhhhh.....ee....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh....eeeeehhhhhhhhh......eee......eeeeee..ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i56 B   5 DDNHLSIVTLEEAPFVIVEDIDPLTETCVRNTVPCRKFVKINNSTNEGMNVKKCCKGFCIDILKKLSRTVKFTYDLYLVTNGKHGKKVNNVWNGMIGEVVYQRAVMAVGSLTINEERSEVVDFSVPFVETGISVMVSRGTQVTGLSDKKFQRPHDYSPPFRFGTVPNGSTERNIRNNYPYMHQYMTRFNQRGVEDALVSLKTGKLDAFIYDAAVLNYKAGRDEGCKLVTIGSGYIFATTGYGIALQKGSPWKRQIDLALLQFVGDGEMEELETLWLTGICE 801
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284|
                                                                                                                                                                                                                                                                                                                 284|
                                                                                                                                                                                                                                                                                                                  801
   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 5I56)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5I56)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5I56)

(-) 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 ]  
    Glu A:405 - Cys A:406   [ RasMol ]  
    Gly B:235 - Ser B:236   [ RasMol ]  
    Ser B:161 - Pro B:162   [ RasMol ]  
    Val A:98 - Asn A:99   [ RasMol ]  
 

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  5i56
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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 5i57 5i58 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 5i57 5i58 5i59 5jty 5u8c 5vih 5vii 5vij

(-) Related Entries Specified in the PDB File

5i57 5i58 5i59