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(-) Description

Title :  CRYSTAL STRUCTURE OF GLUN1/GLUN2A LIGAND-BINDING DOMAIN IN COMPLEX WITH DCKA AND GLUTAMATE
 
Authors :  J. Annie, N. Tajima, H. Furukawa
Date :  30 Oct 13  (Deposition) - 12 Mar 14  (Release) - 12 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Receptor, Dcka And Glutamate, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Jespersen, N. Tajima, G. Fernandez-Cuervo, E. C. Garnier-Amblard H. Furukawa
Structural Insights Into Competitive Antagonism In Nmda Receptors.
Neuron V. 81 366 2014
PubMed-ID: 24462099  |  Reference-DOI: 10.1016/J.NEURON.2013.11.033

(-) Compounds

Molecule 1 - GLUTAMATE RECEPTOR IONOTROPIC, NMDA 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22
    Expression System Strain: ORIGAMIB (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: LIGAND-BINDING DOMAIN, UNP RESIDUES 393-543
    Gene: GRIN1, NMDAR1, RAT GLUN1
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
 
Molecule 2 - GLUTAMATE RECEPTOR IONOTROPIC, NMDA 2A
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: LIGAND-BINDING DOMAIN
    Gene: GRIN2A
    Mutation: YES
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
12JK1Ligand/Ion4-HYDROXY-5,7-DIMETHYLQUINOLINE-2-CARBOXYLIC ACID
2GLU1Mod. Amino AcidGLUTAMIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
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 , ASP A:224 , VAL A:227 , PHE A:250 , HOH A:428 , HOH A:445 , HOH A:450 , HOH A:503 , HOH A:692BINDING SITE FOR RESIDUE 2JK A 301
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:410 , HOH B:429BINDING SITE FOR RESIDUE GLU B 301

(-) 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
2Lys A:235 -Cys A:236
3Ala B:17 -Pro B:18
4Ser B:161 -Pro B:162

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NF4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NF4)

(-) Exons   (0, 0)

(no "Exon" information available for 4NF4)

(-) 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:277
                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4nf4a_ A: N-methyl-D-aspartate receptor subunit 1                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.......eeee....................eeeeee.......eeeeeeehhhhhhhhhhhhhhh..eeeee........ee....eehhhhhhhhh....ee......hhhhhh..ee....eeeeeeeeee.........hhhhhh......ee....hhhhhhhhhh..hhhhhhhhhh....hhhhhhhhhhh....eeeeehhhhhhhhh....eeeeeeeeeeeee..ee.....hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nf4 A   4 TRLKIVTIHQEPFVYVKPTMSDGTCKEEFTVNGDPVKKVICTGPNDGSPRHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKGTRITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRY 287
                                    13        23        33        43     || 56        66        76        86        96 ||    110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       
                                                                        49|                                           98|                                                                                                                                                                                        
                                                                         53                                           103                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4nf4b_ B: automated matches                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......eeee............eeeeeeee.......eeeeeeeeehhhhhhhhhhhhhhh.eeeeee........ee..eehhhhhhhhh....ee......hhhhhh..ee....eeeeeeeeee.........hhhhhh.........ee....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh....eeeeehhhhhhhhh......eee....eeeeee..ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nf4 B   6 DNHLSIVTLEEAPFVIVEDIDPLTETCVRNTVPCRKFVKINNSTNEGMNVKKCCKGFCIDILKKLSRTVKFTYDLYLVTNGKHGKKVNNVWNGMIGEVVYQRAVMAVGSLTINEERSEVVDFSVPFVETGISVMVSRGTQVTGLSDKKFQRPHDYSPPFRFGTVPNGSTERNIRNNYPYMHQYMTRFNQRGVEDALVSLKTGKLDAFIYDAAVLNYKAGRDEGCKLVTIGYIFATTGYGIALQKGSPWKRQIDLALLQFVGDGEMEELETLWLTGICE 301
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235|      247       257       267       277      ||
                                                                                                                                                                                                                                                               235|                                           284|
                                                                                                                                                                                                                                                                238                                            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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NF4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NF4)

(-) 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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  4nf4
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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 4nf5 4nf6 4nf8 5ddn 5ddx 5de4 5dex 5i56 5i57 5i58 5i59 5jty 5tpw 5tq0 5tq2 5vih 5vii 5vij
        NMDZ1_RAT | P35439: 1pb7 1pb8 1pb9 1pbq 1y1m 1y1z 1y20 2a5t 3q41 4kcc 4kfq 4nf5 4nf6 4nf8 4pe5 5ddn 5ddx 5de4 5dex 5fxg 5fxh 5fxi 5fxj 5fxk 5i56 5i57 5i58 5i59 5jty 5u8c 5vih 5vii 5vij

(-) Related Entries Specified in the PDB File

4nf5 4nf6 4nf8