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(-) Description

Title :  CRYSTAL STRUCTURE OF THE GLUA2 LIGAND-BINDING DOMAIN (S1S2J-L483Y-N754S) IN COMPLEX WITH GLUTAMATE AND BPAM37 AT 1.56 A RESOLUTION.
 
Authors :  A. B. Noerholm, K. Frydenvang, J. S. Kastrup
Date :  24 Jul 14  (Deposition) - 19 Nov 14  (Release) - 11 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.56
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ampa Receptor Ligand-Binding Domain, Bpam37 Allosteric Modulation, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Francotte, A. B. Nrholm, T. Deva, L. Olsen, K. Frydenvang, E. Goffin P. Fraikin, P. De Tullio, S. Challal, J. Y. Thomas, F. Iop, C. Louis, I. Botez-Pop, P. Lestage, L. Danober, J. S. Kastrup, B. Pirotte
Positive Allosteric Modulators Of 2-Amino-3-(3-Hydroxy-5-Methylisoxazol-4-Yl)Propionic Acid Receptors Belonging To 4-Cyclopropyl-3, 4-Dihydro-2H-1, 2, 4-Pyridothiadiazine Dioxides And Diversely Chloro-Substituted 4-Cyclopropyl-3, 4-Dihydro-2H-1, 2, 4-Benzothiadiazine 1, 1-Dioxides.
J. Med. Chem. V. 57 9539 2014
PubMed-ID: 25375781  |  Reference-DOI: 10.1021/JM501268R
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUTAMATE RECEPTOR 2,GLUTAMATE RECEPTOR 2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-22B(+)
    Expression System Strain: ORIGAMI 2
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 413-527, UNP RESIDUES 653-796
    Gene: GRIA2, GLUR2
    Mutation: YES
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: AMPA 2,GLUA2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 18)

Asymmetric/Biological Unit (6, 18)
No.NameCountTypeFull Name
13C22Ligand/Ion4-ETHYL-3,4-DIHYDRO-2H-PYRIDO[3,2-E][1,2,4]THIADIAZINE1,1-DIOXIDE
2ACT4Ligand/IonACETATE ION
3GLU2Mod. Amino AcidGLUTAMIC ACID
4GOL3Ligand/IonGLYCEROL
5PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
6SO45Ligand/IonSULFATE ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:481 , PRO A:494 , SER A:497 , SER A:729 , LYS A:730 , GLY A:731 , LYS B:493 , PRO B:494 , PHE B:495 , MET B:496 , SER B:497 , SER B:754 , 3C2 B:801binding site for residue 3C2 A 801
02AC2SOFTWARESER A:652 , LYS A:656 , ARG A:660 , GOL A:808 , HOH A:1003 , HOH A:1018 , HOH A:1147 , HOH A:1170 , HOH A:1172binding site for residue SO4 A 802
03AC3SOFTWAREGLU A:486 , ASP A:490 , PHE A:491 , HOH A:1132 , LYS B:493 , HOH B:1053binding site for residue SO4 A 803
04AC4SOFTWARETYR A:450 , PRO A:478 , LEU A:479 , THR A:480 , ARG A:485 , GLY A:653 , SER A:654 , THR A:655 , GLU A:705 , TYR A:732 , HOH A:977 , HOH A:978 , HOH A:988binding site for residue GLU A 804
05AC5SOFTWAREASP A:760 , ASN B:726 , ASP B:728 , SER B:729binding site for residue ACT A 805
06AC6SOFTWAREARG A:660 , TRP A:671 , ARG A:675 , GOL A:808 , HOH A:940 , HOH A:943binding site for residue GOL A 806
07AC7SOFTWARELYS A:393 , THR A:394binding site for residue GOL A 807
08AC8SOFTWARELYS A:656 , ARG A:675 , SO4 A:802 , GOL A:806 , HOH A:1205binding site for residue GOL A 808
09AC9SOFTWAREGLU A:416 , GLY A:417 , ARG A:420 , LYS A:441binding site for residue PEG A 809
10AD1SOFTWARETYR A:469 , GLY A:470 , LYS A:471 , LYS A:505 , PRO A:717 , ASP A:719 , HOH A:902binding site for residue PEG A 810
11AD2SOFTWARELYS A:493 , PRO A:494 , PHE A:495 , MET A:496 , SER A:497 , SER A:754 , 3C2 A:801 , PRO B:494 , SER B:497 , SER B:729 , LYS B:730 , GLY B:731binding site for residue 3C2 B 801
12AD3SOFTWAREALA B:452 , SER B:652 , LYS B:656 , ARG B:660 , HOH B:1032 , HOH B:1033 , HOH B:1123 , HOH B:1124binding site for residue SO4 B 802
13AD4SOFTWARELYS A:695 , ARG B:420 , HOH B:911 , HOH B:918 , HOH B:919 , HOH B:991binding site for residue SO4 B 803
14AD5SOFTWARELYS A:493 , HOH A:1080 , GLU B:486 , ASP B:490 , PHE B:491 , HOH B:1081 , HOH B:1100binding site for residue SO4 B 804
15AD6SOFTWARETYR B:450 , PRO B:478 , LEU B:479 , THR B:480 , ARG B:485 , GLY B:653 , SER B:654 , THR B:655 , GLU B:705 , TYR B:732 , HOH B:967 , HOH B:981 , HOH B:992binding site for residue GLU B 805
16AD7SOFTWAREASN A:726 , LEU A:727 , ASP A:728 , SER A:729 , ASP B:760binding site for residue ACT B 806
17AD8SOFTWAREARG B:660 , TRP B:671 , ARG B:675 , HOH B:1166binding site for residue ACT B 807
18AD9SOFTWARETYR A:483 , HIS B:435 , ALA B:749 , HOH B:1029binding site for residue ACT B 808

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:718 -A:773
2B:718 -B:773

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Ser A:403 -Pro A:404
2Glu A:678 -Pro A:679
3Lys A:716 -Pro A:717
4Ser B:403 -Pro B:404
5Glu B:678 -Pro B:679
6Lys B:716 -Pro B:717

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4U4X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4U4X)

(-) Exons   (0, 0)

(no "Exon" information available for 4U4X)

(-) 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:263
                                                                                                                                                                                                                                                                                                       
               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....eee....hhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhh...eeeeeehhhhhhhhh.....eeee......eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u4x A 390 GANKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITYVREEVIDFSKPFMSLGISIMIKKGTPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLSEQGLLDKLKNKWWYDKGECGS 775
                                   399       409       419       429       439       449       459       469       479       489       499       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772   
                                                                                                                                                508|                                                                                                                                               
                                                                                                                                                 632                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:259
                                                                                                                                                                                                                                                                                                   
               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....hhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u4x B 393 KTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITYVREEVIDFSKPFMSLGISIMIKKGTPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLSEQGLLDKLKNKWWYDKGECG 774
                                   402       412       422       432       442       452       462       472       482       492       502     ||635       645       655       665       675       685       695       705       715       725       735       745       755       765         
                                                                                                                                             508|                                                                                                                                              
                                                                                                                                              632
   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 4U4X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4U4X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4U4X)

(-) Gene Ontology  (49, 49)

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
        GRIA2_RAT | P19491: 1ftj 1ftk 1ftl 1ftm 1fto 1fw0 1gr2 1lb8 1lb9 1lbb 1lbc 1m5b 1m5c 1m5d 1m5e 1m5f 1mm6 1mm7 1mqd 1mqg 1mqh 1mqi 1mqj 1ms7 1mxu 1mxv 1mxw 1mxx 1mxy 1mxz 1my0 1my1 1my2 1my3 1my4 1n0t 1nnk 1nnp 1p1n 1p1o 1p1q 1p1u 1p1w 1syh 1syi 1wvj 1xhy 2aix 2al4 2al5 2anj 2cmo 2gfe 2i3v 2i3w 2p2a 2uxa 2xx7 2xx8 2xx9 2xxh 2xxi 3b6q 3b6t 3b6w 3b7d 3bbr 3bft 3bfu 3bki 3dp6 3h03 3h06 3h5v 3h5w 3h6t 3h6u 3h6v 3h6w 3hsy 3ijo 3ijx 3ik6 3il1 3ilt 3ilu 3kg2 3kgc 3lsf 3lsl 3m3l 3n6v 3o28 3o29 3o2a 3o2j 3o6g 3o6h 3o6i 3pd8 3pd9 3pmv 3pmw 3pmx 3rtf 3rtw 3t93 3t96 3t9h 3t9u 3t9v 3t9x 3tdj 3tkd 3tza 4fat 4g8m 4gxs 4h8j 4igt 4isu 4iy5 4iy6 4l17 4lz5 4lz7 4lz8 4n07 4o3a 4o3b 4o3c 4q30 4u1o 4u1w 4u1x 4u1y 4u1z 4u21 4u22 4u23 4u2p 4u2q 4u2r 4u4f 4u4g 4u4s 4u5b 4u5c 4u5d 4u5e 4u5f 4uq6 4uqj 4uqk 4x48 4yma 4yu0 4z0i 5buu 5cbr 5cbs 5elv 5fhm 5fhn 5fho 5fth 5fti 5fwx 5fwy 5ide 5idf 5jei 5kbs 5kbt 5kbu 5kbv 5kk2 5l1b 5l1e 5l1f 5l1g 5l1h 5vhw 5vhx 5vhy 5vhz 5vot 5vou 5vov

(-) Related Entries Specified in the PDB File

3tdj 3TDJ CONTAINS THE SAME PROTEIN COMPLEXED WITH BPAM97.
4n07 4N07 CONTAINS THE SAME PROTEIN COMPLEXED WITH BPAM344.