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(-) Description

Title :  CRYSTAL STRUCTURE OF THE GLUA2 LIGAND-BINDING DOMAIN (S1S2J-L504-N775) IN COMPLEX WITH GLUTAMATE AND BPAM-521 AT 1.92 A RESOLUTION
 
Authors :  C. Krintel, L. Juknaite, K. Frydenvang, J. S. Kastrup
Date :  05 Nov 15  (Deposition) - 04 May 16  (Release) - 22 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.92
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ampa Receptor Ligand-Binding Domain, Bpam-521 Allosteric Modulation, Membrane Protein, Fusion Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Krintel, P. Francotte, D. S. Pickering, L. Juknaite, J. Phlsgaard, L. Olsen, K. Frydenvang, E. Goffin, B. Pirotte, J. S. Kastrup
Enthalpy-Entropy Compensation In The Binding Of Modulators At Ionotropic Glutamate Receptor Glua2.
Biophys. J. V. 110 2397 2016
PubMed-ID: 27276258  |  Reference-DOI: 10.1016/J.BPJ.2016.04.032
(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
    Expression System Plasmid: PET-22B(+)
    Expression System Strain: ORIGAMI B (DE3)
    Expression System Taxid: 562
    Fragment: UNP RESIDUES, 413-527,UNP RESIDUE, 653-797
    Gene: GRIA2, GLUR2
    Mutation: YES
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Other Details: THE PROTEIN COMPRISES SEGMENT S1 RESIDUES 413-527, A GT LINKER AND S2 RESIDUES 653-798.
    Synonym: GLUR-2,AMPA-SELECTIVE GLUTAMATE RECEPTOR 2,GLUR-B,GLUR-K2, GLUTAMATE RECEPTOR IONOTROPIC,AMPA 2,GLUA2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 26)

Asymmetric/Biological Unit (7, 26)
No.NameCountTypeFull Name
15PX2Ligand/Ion4-CYCLOPROPYL-3,4-DIHYDRO-7-HYDROXY-2H-1,2,4-BENZOTHIADIAZINE 1,1-DIOXIDE
2ACT9Ligand/IonACETATE ION
3CL3Ligand/IonCHLORIDE ION
4GLU2Mod. Amino AcidGLUTAMIC ACID
5GOL4Ligand/IonGLYCEROL
6PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
7SO44Ligand/IonSULFATE ION

(-) Sites  (26, 26)

Asymmetric Unit (26, 26)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:140 , LYS A:144 , ARG A:148 , HOH A:404 , HOH A:409 , HOH A:541binding site for residue SO4 A 301
02AC2SOFTWAREARG A:31 , HOH A:408 , HOH A:422 , HOH A:456 , HOH A:461 , LYS B:183binding site for residue SO4 A 302
03AC3SOFTWAREARG A:149 , HOH A:474 , LYS B:240binding site for residue SO4 A 303
04AC4SOFTWAREARG A:148 , TRP A:159 , ARG A:163 , HOH A:558binding site for residue GOL A 304
05AC5SOFTWARESER A:108 , SER A:194 , THR A:195 , GLU A:198 , ASN A:214 , HOH A:465binding site for residue GOL A 305
06AC6SOFTWAREARG A:163 , HOH B:577binding site for residue CL A 306
07AC7SOFTWARELYS A:21 , ASN A:22binding site for residue CL A 307
08AC8SOFTWAREALA A:153 , LYS B:249binding site for residue ACT A 308
09AC9SOFTWAREASP A:257 , HOH A:431binding site for residue ACT A 309
10AD1SOFTWAREASP A:248 , ASN B:214 , ASP B:216 , SER B:217binding site for residue ACT A 310
11AD2SOFTWAREASP A:38 , GLU A:42 , LEU A:250 , LYS A:253 , LYS B:21binding site for residue ACT A 311
12AD3SOFTWAREPRO A:105 , SER A:108 , SER A:217 , LYS A:218 , GLY A:219 , HOH A:545 , LYS B:104 , PRO B:105 , PHE B:106 , MET B:107 , SER B:108 , SER B:242 , 5PX B:312binding site for residue 5PX A 312
13AD4SOFTWARETYR 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:437 , HOH A:444 , HOH A:473binding site for residue GLU A 313
14AD5SOFTWARESER B:140 , LYS B:144 , ARG B:148 , HOH B:411 , HOH B:430 , HOH B:458binding site for residue SO4 B 301
15AD6SOFTWARESER B:108 , SER B:194 , GLU B:198 , ASN B:214 , HOH B:407binding site for residue GOL B 302
16AD7SOFTWAREARG B:148 , TRP B:159 , ARG B:163 , ACT B:307binding site for residue GOL B 303
17AD8SOFTWARELYS B:4 , THR B:5binding site for residue CL B 304
18AD9SOFTWARELYS B:82 , LYS B:116binding site for residue ACT B 305
19AE1SOFTWAREASP B:58 , LYS B:60 , ASN B:72binding site for residue ACT B 306
20AE2SOFTWARELYS B:144 , ARG B:163 , GOL B:303binding site for residue ACT B 307
21AE3SOFTWARESER B:123 , ALA B:124 , GLY B:213 , HOH B:422binding site for residue ACT B 308
22AE4SOFTWARETYR A:94 , HIS B:46 , ALA B:237 , LYS B:240 , HOH B:504binding site for residue ACT B 309
23AE5SOFTWAREGLU B:27 , GLY B:28 , ARG B:31 , LYS B:52 , HOH B:453binding site for residue PEG B 310
24AE6SOFTWAREARG A:203 , LYS A:258 , HIS B:23 , ARG B:31binding site for residue PEG B 311
25AE7SOFTWARELYS A:104 , PRO A:105 , PHE A:106 , MET A:107 , SER A:108 , SER A:242 , 5PX A:312 , PRO B:105 , SER B:108 , SER B:217 , LYS B:218 , GLY B:219binding site for residue 5PX B 312
26AE8SOFTWARETYR B:61 , PRO B:89 , LEU B:90 , THR B:91 , ARG B:96 , GLY B:141 , SER B:142 , THR B:143 , GLU B:193 , HOH B:462 , HOH B:465 , HOH B:467binding site for residue GLU B 313

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:206 -A:261
2B:206 -B:261

(-) Cis Peptide Bonds  (6, 6)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ELV)

(-) 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 ....eeeeee.......ee..hhhhhhhhh.eehhhhhhhhhhhhhhh.eeeeee................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
                 5elv A   1 GANKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITYVREEVIDFSKPFMSLGISIMIKKGTPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLSEQGLLDKLKNKWWYDKGECGS 263
                                    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   


Chain B 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...eeeeeehhhhhhhh......eeee......eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5elv B   1 GANKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITYVREEVIDFSKPFMSLGISIMIKKGTPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLSEQGLLDKLKNKWWYDKGECGS 263
                                    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
   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 5ELV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 4u4x 4u5b 4u5c 4u5d 4u5e 4u5f 4uq6 4uqj 4uqk 4x48 4yma 4yu0 4z0i 5buu 5cbr 5cbs 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

3il1 3IL1 IS THE GLUA2 LBD IN COMPLEX WITH THE STRUCTURALLY RELATED MODULATOR IDRA-21.
3tdj 3TDJ IS THE SAME PROTEIN IN COMPLEX WITH THE STRUCTURALLY RELATED MODULATOR BPAM97.
3tdk 3TDK IS THE SAME PROTEIN IN COMPLEX WITH THE STRUCTURALLY RELATED MODULATOR CYCLOTHIAZIDE.
4n07 4N07 IS THE SAME PROTEIN IN COMPLEX WITH THE STRUCTURALLY RELATED MODULATOR BPAM344.
4u4s 4U4S IS THE SAME PROTEIN IN COMPLEX WITH THE STRUCTURALLY RELATED MODULATOR BPAM25.
4u4x 4U4X IS THE SAME PROTEIN IN COMPLEX WITH THE STRUCTURALLY RELATED MODULATOR BPAM37.