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(-) Description

Title :  STRUCTURE OF THE HUMAN GLUA2 LBD IN COMPLEX WITH GNE3419
 
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 :  1.70
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C  (2x)
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 2,GLUTAMATE RECEPTOR 2
    Chains: A, C, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 413-527, GT LINKER, UNP RESIDUES 653-796
    Gene: GRIA2, GLUR2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GLUR-2, AMPA-SELECTIVE GLUTAMATE RECEPTOR 2, GLUR-B, GLUR- K2, GLUTAMATE RECEPTOR IONOTROPIC, AMPA 2, GLUA2

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): AB 
Biological Unit 2 (2x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric Unit (4, 12)
No.NameCountTypeFull Name
15YC2Ligand/Ion7-[[ETHYL(PHENYL)AMINO]METHYL]-2-METHYL-[1,3,4]THIADIAZOLO[3,2-A]PYRIMIDIN-5-ONE
2CAC1Ligand/IonCACODYLATE ION
3GLU3Mod. Amino AcidGLUTAMIC ACID
4ZN6Ligand/IonZINC ION
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
15YC1Ligand/Ion7-[[ETHYL(PHENYL)AMINO]METHYL]-2-METHYL-[1,3,4]THIADIAZOLO[3,2-A]PYRIMIDIN-5-ONE
2CAC1Ligand/IonCACODYLATE ION
3GLU2Mod. Amino AcidGLUTAMIC ACID
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
15YC2Ligand/Ion7-[[ETHYL(PHENYL)AMINO]METHYL]-2-METHYL-[1,3,4]THIADIAZOLO[3,2-A]PYRIMIDIN-5-ONE
2CAC-1Ligand/IonCACODYLATE ION
3GLU2Mod. Amino AcidGLUTAMIC ACID
4ZN-1Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:61 , PRO A:89 , LEU A:90 , THR A:91 , ARG A:96 , GLY A:141 , SER A:142 , THR A:143 , GLU A:193 , HOH A:428 , HOH A:444 , HOH A:466binding site for residue GLU A 301
02AC2SOFTWAREPRO A:105 , MET A:107 , SER A:108 , SER A:217 , LYS A:218 , GLY A:219 , SER A:242 , HOH A:494 , HOH A:528 , ILE B:92 , PRO B:105 , MET B:107 , SER B:108 , SER B:217 , LYS B:218 , GLY B:219 , HOH B:454 , HOH B:477 , HOH B:490binding site for residue 5YC A 302
03AC3SOFTWAREGLU A:42 , HIS A:46 , CAC A:305 , GLU C:166binding site for residue ZN A 303
04AC4SOFTWAREHIS A:23 , HOH A:579 , ASP B:65 , HOH B:526binding site for residue ZN A 304
05AC5SOFTWAREGLU A:42 , HIS A:46 , ZN A:303 , HOH A:401 , ARG C:163 , ALA C:165 , GLU C:166 , SER C:168 , PHE C:170binding site for residue CAC A 305
06AC6SOFTWARETYR C:61 , PRO C:89 , LEU C:90 , THR C:91 , ARG C:96 , GLY C:141 , SER C:142 , THR C:143 , GLU C:193 , TYR C:220 , HOH C:469 , HOH C:504 , HOH C:509binding site for residue GLU C 301
07AC7SOFTWAREILE C:92 , PRO C:105 , MET C:107 , SER C:108 , SER C:217 , LYS C:218 , GLY C:219 , HOH C:419 , HOH C:496 , HOH C:549binding site for residue 5YC C 302
08AC8SOFTWAREHIS B:23 , HIS C:23 , GLU C:30 , HOH C:618binding site for residue ZN C 303
09AC9SOFTWAREGLU A:166 , GLU C:42 , HIS C:46 , LEU C:241 , HOH C:607binding site for residue ZN C 304
10AD1SOFTWARETYR B:61 , PRO B:89 , LEU B:90 , THR B:91 , ARG B:96 , LEU B:138 , GLY B:141 , SER B:142 , THR B:143 , GLU B:193 , TYR B:220 , HOH B:431 , HOH B:447 , HOH B:452binding site for residue GLU B 301
11AD2SOFTWAREGLU B:42 , LYS B:45 , HIS B:46 , HOH B:488binding site for residue ZN B 302
12AD3SOFTWAREASP B:156binding site for residue ZN B 303

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:206 -A:261
2B:206 -B:261
3C:206 -C:261

(-) Cis Peptide Bonds  (9, 9)

Asymmetric Unit
No.Residues
1Ser A:14 -Pro A:15
2Glu A:166 -Pro A:167
3Lys A:204 -Pro A:205
4Ser C:14 -Pro C:15
5Glu C:166 -Pro C:167
6Lys C:204 -Pro C:205
7Ser B:14 -Pro B:15
8Glu B:166 -Pro B:167
9Lys B:204 -Pro B:205

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5H8S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5H8S)

(-) Exons   (0, 0)

(no "Exon" information available for 5H8S)

(-) Sequences/Alignments

Asymmetric 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:260
                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.......ee..hhhhhhhhh.eehhhhhhhhhhhhhhh..eeeee................hhhhhhhhh....ee......hhhhhh.eee....eee.eeeeee......hhhhhhh....eeee...hhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhh...eeeeeehhhhhhhhh.....eeee......eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h8s A   3 NKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKGTPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLSEQGLLDKLKNKWWYDKGECE 301
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       301
                                                                                                                                                                                                                                                                                            261|
                                                                                                                                                                                                                                                                                             301


Chain B from PDB  Type:PROTEIN  Length:260
                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.......ee..hhhhhhhhh.eehhhhhhhhhhhhhhh..eeeee................hhhhhhhhh....ee......hhhhhh.eee....eee.eeeeee......hhhhhhh....eeee...hhhhhhhhh..hhhhhhhhhhhhhh.......hhhhhhhhhhhh...eeeeeehhhhhhhhh.....eeee......eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h8s B   3 NKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKGTPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLSEQGLLDKLKNKWWYDKGECE 301
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       301
                                                                                                                                                                                                                                                                                            261|
                                                                                                                                                                                                                                                                                             301


Chain C from PDB  Type:PROTEIN  Length:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.......ee........hhh.eehhhhhhhhhhhhhhh..eeeee................hhhhhhhhh....ee......hhhhhh.eee....eee.eeeeee......hhhhhhh....eeee...hhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhh...eeeeeehhhhhhhhh.....eeee......eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h8s C   1 GSNKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKGTPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLSEQGLLDKLKNKWWYDKGECGE 301
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260 ||
                                                                                                                                                                                                                                                                                               262|
                                                                                                                                                                                                                                                                                                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 5H8S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5H8S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5H8S)

(-) Gene Ontology  (24, 24)

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 Related Entries

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        GRIA2_HUMAN | P42262: 2wjw 2wjx 2xhd 3r7x 3rn8 3rnn 3ua8

(-) Related Entries Specified in the PDB File

5h8f 5h8h 5h8n 5h8q 5h8r