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(-) Description

Title :  STRUCTURE OF THE APO HUMAN GLUN1/GLUN2A LBD
 
Authors :  H. J. A. Wallweber, P. J. Lupardus
Date :  23 Dec 15  (Deposition) - 24 Feb 16  (Release) - 24 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.81
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Glun1, Glun2A, Nmda, Receptor, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. H. Hackos, P. J. Lupardus, T. Grand, Y. Chen, T. -M. Wang, P. Reynen, A. Gustafson, H. J. A. Wallweber, M. Volgraf, B. D. Sellers, J. B. Schwarz, P. Paoletti, M. Sheng, Q. Zhou, J. E. Hanson
Positive Allosteric Modulators Of Glun2A-Containing Nmdars With Distinct Modes Of Action And Impacts On Circuit Function
Neuron V. 89 1 2016
PubMed: search  |  Reference-DOI: 10.1016/J.NEURON.2016.01.016

(-) Compounds

Molecule 1 - GLUTAMATE RECEPTOR IONOTROPIC, NMDA 2A
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 401-539, GT LINKER, UNP RESIDUES 661-802
    Gene: GRIN2A, NMDAR2A
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GLUN2A, GLUTAMATE [NMDA] RECEPTOR SUBUNIT EPSILON-1, N- METHYL D-ASPARTATE RECEPTOR SUBTYPE 2A, HNR2A
 
Molecule 2 - GLUTAMATE RECEPTOR IONOTROPIC, NMDA 1
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 394-544, GT LINKER, UNP RESIDUES 663-800
    Gene: GRIN1, NMDAR1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GLUN1, GLUTAMATE [NMDA] RECEPTOR SUBUNIT ZETA-1, N-METHYL-D- ASPARTATE RECEPTOR SUBUNIT NR1, NMD-R1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1GLU1Mod. Amino AcidGLUTAMIC ACID
2GLY1Mod. Amino AcidGLYCINE
3GOL6Ligand/IonGLYCEROL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:238 , PHE A:239 , ALA A:240 , THR A:241 , HOH A:437 , HIS B:273 , GLU B:279 , HOH B:460binding site for residue GOL A 301
2AC2SOFTWAREHIS A:87 , SER A:113 , THR A:115 , ARG A:120 , GLY A:171 , SER A:172 , THR A:173 , TYR A:213 , ASP A:214 , HOH A:455 , HOH A:521binding site for residue GLU A 302
3AC3SOFTWARETHR B:28 , CYS B:29 , LYS B:42 , HOH B:530 , HOH B:542binding site for residue GOL B 301
4AC4SOFTWARETHR B:34 , VAL B:35 , THR B:284 , TRP B:285 , HOH B:432binding site for residue GOL B 302
5AC5SOFTWARETHR B:34 , ASP B:38 , PRO B:39 , LYS B:41 , ASP B:70binding site for residue GOL B 303
6AC6SOFTWAREASP B:120 , ARG B:256 , SER B:259 , PRO B:260 , TRP B:261 , HOH B:402 , HOH B:516binding site for residue GOL B 304
7AC7SOFTWAREASP A:259 , ALA B:133 , ILE B:136 , GLU B:137 , PHE B:138 , LYS B:257 , HOH B:422binding site for residue GOL B 305
8AC8SOFTWAREPHE B:93 , PRO B:125 , LEU B:126 , THR B:127 , ARG B:132 , SER B:180 , SER B:181 , ASP B:225binding site for residue GLY B 306

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:31 -A:57
2A:38 -A:58
3A:228 -A:283
4B:29 -B:63
5B:45 -B:64
6B:237 -B:291

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ala A:16 -Pro A:17
2Ser A:160 -Pro A:161
3Glu B:15 -Pro B:16

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5H8F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5H8F)

(-) Exons   (0, 0)

(no "Exon" information available for 5H8F)

(-) 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:274
                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......eeee........eeeeeeee.......eeeeeeeeehhhhhhhhhhhhhhh.eeeeee........ee..eehhhhhhhhh....ee......hhhhhh..ee....eeeeeeeeee.........hhhhhhhhhh.....ee....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh....eeeeehhhhhhhhhh.....eee......eeeeee..ee.....hhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h8f A   6 NHLSIVTLEEAPFVIVEDIETCVRNTVPCRKFVKINNSTNEGMNVKKCCKGFCIDILKKLSRTVKFTYDLYLVTNGKHGKKVNNVWNGMIGEVVYQRAVMAVGSLTINEERSEVVDFSVPFVETGISVMVSRGTQVTGLSDKKFQRPHDYSPPFRFGTVPNGSTERNIRNNYPYMHQYMTKFNQKGVEDALVSLKTGKLDAFIYDAAVLNYKAGRDEGCKLVTIGSGYIFATTGYGIALQKGSPWKRQIDLALLQFVGDGEMEELETLWLTGIC 283
                                    15        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279    
                                             24|                                                                                                                                                                                                                                                              
                                              29                                                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:283
                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.......eeee....................eeeeee..........eeeeeeehhhhhhhhhhhhhhh..eeeee........eee...eeehhhhhhhhh....ee......hhhhhh..ee....eeeeeeeeee.........hhhhhh......ee....hhhhhhhhhh..hhhhhhhhhh....hhhhhhhhhhh....eeeeehhhhhhhhhhh..eeeeeeeeeeeee..ee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h8f B   6 RLKIVTIHQEPFVYVKPTLSDGTCKEEFTVNGDPVKKVICTGPNDTSPGSPRHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKGTRITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQEC 291
                                    15        25        35        45        55        65        75        85        95   ||  108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288   
                                                                                                                        99|                                                                                                                                                                                            
                                                                                                                        103
   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 5H8F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5H8F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5H8F)

(-) Gene Ontology  (122, 165)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        NMDE1_HUMAN | Q12879: 3nfl 5h8h 5h8n 5h8q 5i2k 5i2n 5kcj 5kdt 5tp9 5tpa
        NMDZ1_HUMAN | Q05586: 2hqw 2nr1 3bya 5h8h 5h8n 5h8q 5i2k 5i2n 5kcj 5kdt 5tp9 5tpa

(-) Related Entries Specified in the PDB File

5h8h 5h8n 5h8q 5h8r 5h8s