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(-) Description

Title :  CRYSTAL STRUCTURE OF THE GLUA2 LIGAND-BINDING DOMAIN (S1S2J) IN COMPLEX WITH THE ANTAGONIST (R)-2-AMINO-3-(3'-HYDROXYBIPHENYL-3-YL) PROPANOIC ACID AT 1.8A RESOLUTION
 
Authors :  K. Frydenvang, J. S. Kastrup
Date :  01 Jul 15  (Deposition) - 30 Dec 15  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Ampa Receptor Ligand-Binding Domain, Glua2-S1S2J, Antagonist, Membrane Protein, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Szymanska, K. Frydenvang, D. S. Pickering, C. Krintel, B. Nielsen, A. Kooshki, L. G. Zachariassen, L. Olsen, J. S. Kastrup, T. N. Johansen
Studies On Aryl-Substituted Phenylalanines: Synthesis, Activity, And Different Binding Modes At Ampa Receptors.
J. Med. Chem. V. 59 448 2016
PubMed-ID: 26653877  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B01666

(-) Compounds

Molecule 1 - GLUTAMATE RECEPTOR 2,GLUTAMATE RECEPTOR 2
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-22B(+)
    Expression System Taxid: 469008
    Expression System Variant: ORIGAMI B
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 413-527,UNP RESIDUES 653-797
    Gene: GRIA2, GLUR2
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: GLUR-2,AMPA-SELECTIVE GLUTAMATE RECEPTOR 2,GLUR-B,GLUR-K2, GLUTAMATE RECEPTOR IONOTROPIC,AMPA 2,GLUA2,GLUR-2,AMPA-SELECTIVE GLUTAMATE RECEPTOR 2,GLUR-B,GLUR-K2,GLUTAMATE RECEPTOR IONOTROPIC, AMPA 2,GLUA2

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 33)

Asymmetric Unit (5, 33)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2E424Ligand/Ion(R)-2-AMINO-3-(3'-HYDROXYBIPHENYL-3-YL)PROPANOIC ACID
3EDO14Ligand/Ion1,2-ETHANEDIOL
4GOL4Ligand/IonGLYCEROL
5SO410Ligand/IonSULFATE ION
Biological Unit 1 (4, 14)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2E422Ligand/Ion(R)-2-AMINO-3-(3'-HYDROXYBIPHENYL-3-YL)PROPANOIC ACID
3EDO4Ligand/Ion1,2-ETHANEDIOL
4GOL3Ligand/IonGLYCEROL
5SO45Ligand/IonSULFATE ION
Biological Unit 2 (4, 18)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2E422Ligand/Ion(R)-2-AMINO-3-(3'-HYDROXYBIPHENYL-3-YL)PROPANOIC ACID
3EDO10Ligand/Ion1,2-ETHANEDIOL
4GOL1Ligand/IonGLYCEROL
5SO45Ligand/IonSULFATE ION

(-) Sites  (33, 33)

Asymmetric Unit (33, 33)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:58 , PRO A:86 , LEU A:87 , THR A:88 , ARG A:93 , ILE A:108 , SER A:139 , GLU A:190 , ASP A:213 , LYS A:215 , TYR A:217 , EDO A:304 , HOH A:450 , HOH A:541binding site for residue E42 A 301
02AC2SOFTWARELYS A:47 , ARG A:145 , TRP A:156 , ARG A:160binding site for residue SO4 A 302
03AC3SOFTWAREMET A:16 , HIS A:20 , GLU A:21 , ARG A:28 , HOH A:425 , HOH A:474 , HOH A:624 , HIS C:43binding site for residue SO4 A 303
04AC4SOFTWARETYR A:58 , GLU A:190 , TYR A:217 , E42 A:301 , HOH A:429 , HOH A:445 , HOH A:475binding site for residue EDO A 304
05AC5SOFTWAREPRO A:102 , PHE A:103 , MET A:104 , SER A:105 , ASN A:239 , HOH A:412 , HOH A:629 , SER C:214binding site for residue EDO A 305
06AC6SOFTWARESER A:137 , GLY A:138 , HOH A:437 , HOH A:519binding site for residue EDO A 306
07AC7SOFTWARELYS A:113 , HOH A:410 , LYS D:79binding site for residue EDO A 307
08AC8SOFTWAREGLU A:24 , GLY A:25 , ARG A:28 , LYS A:49 , HOH A:604 , HOH A:615 , GLN C:241binding site for residue GOL A 308
09AC9SOFTWARETYR B:58 , PRO B:86 , LEU B:87 , THR B:88 , ARG B:93 , ILE B:108 , SER B:139 , GLU B:190 , ASP B:213 , LYS B:215 , EDO B:304 , HOH B:422 , HOH B:557binding site for residue E42 B 301
10AD1SOFTWAREHIS B:20 , GLU B:21 , ARG B:28 , HIS B:43 , HOH B:471binding site for residue SO4 B 302
11AD2SOFTWAREARG B:145 , TRP B:156 , ARG B:160 , LYS D:47binding site for residue SO4 B 303
12AD3SOFTWARETYR B:58 , GLU B:190 , TYR B:217 , E42 B:301 , HOH B:443 , HOH B:573binding site for residue EDO B 304
13AD4SOFTWARESER B:214 , HOH B:555 , PRO D:102 , SER D:105 , ASN D:239 , EDO D:307 , HOH D:425binding site for residue EDO B 305
14AD5SOFTWAREPRO B:102 , PHE B:103 , MET B:104 , SER B:105 , HOH B:412 , HOH B:535 , HOH B:580 , SER D:214 , HOH D:401binding site for residue EDO B 306
15AD6SOFTWARESER B:137 , GLY B:138 , HOH B:437 , HOH B:477binding site for residue EDO B 307
16AD7SOFTWARESER B:105 , SER B:191 , GLU B:195 , ASN B:211 , HOH B:519 , HOH B:609binding site for residue EDO B 308
17AD8SOFTWAREGLU B:24 , GLY B:25 , ARG B:28 , LYS B:49 , HOH B:603 , ARG D:146 , LYS D:148 , HOH D:629binding site for residue GOL B 309
18AD9SOFTWARETYR C:58 , PRO C:86 , LEU C:87 , THR C:88 , ARG C:93 , LEU C:106 , ILE C:108 , SER C:139 , GLU C:190 , ASP C:213 , TYR C:217 , HOH C:424 , HOH C:443binding site for residue E42 C 301
19AE1SOFTWAREHIS A:43 , HIS C:20 , GLU C:21 , ARG C:28 , GOL C:305 , HOH C:434binding site for residue SO4 C 302
20AE2SOFTWARESER C:105 , SER C:191 , GLU C:195 , ASN C:211 , LYS C:248 , HOH C:478 , HOH C:629binding site for residue SO4 C 303
21AE3SOFTWAREARG C:145 , TRP C:156 , ARG C:160binding site for residue SO4 C 304
22AE4SOFTWAREHIS A:43 , LYS A:237 , GLN A:241 , LEU C:23 , ARG C:28 , SO4 C:302 , HOH C:434 , HOH C:594binding site for residue GOL C 305
23AE5SOFTWARELYS C:17 , ASN C:26 , GLU C:27 , TYR C:29 , GLU C:30 , VAL C:34 , HOH C:429 , HOH C:439 , HOH C:445binding site for residue GOL C 306
24AE6SOFTWARESER C:137 , GLY C:138 , HOH C:627binding site for residue CL C 307
25AE7SOFTWARETYR D:58 , PRO D:86 , LEU D:87 , THR D:88 , ARG D:93 , ILE D:108 , SER D:139 , GLU D:190 , ASP D:213 , LYS D:215 , TYR D:217 , EDO D:305 , HOH D:411 , HOH D:547binding site for residue E42 D 301
26AE8SOFTWARESER D:105 , SER D:191 , GLU D:195 , ASN D:211 , HOH D:492binding site for residue SO4 D 302
27AE9SOFTWAREHIS D:20 , GLU D:21 , ARG D:28 , HIS D:43 , HOH D:466 , HOH D:476 , HOH D:561binding site for residue SO4 D 303
28AF1SOFTWAREARG D:145 , TRP D:156 , ARG D:160 , HOH D:552binding site for residue SO4 D 304
29AF2SOFTWARETYR D:58 , GLU D:190 , MET D:193 , TYR D:217 , E42 D:301 , HOH D:416 , HOH D:555binding site for residue EDO D 305
30AF3SOFTWARESER D:137 , GLY D:138 , HOH D:464 , HOH D:572binding site for residue EDO D 306
31AF4SOFTWAREEDO B:305 , MET D:104 , SER D:105 , ASP D:245 , HOH D:402 , HOH D:407 , HOH D:425binding site for residue EDO D 307
32AF5SOFTWAREMET D:15 , MET D:16 , HOH D:405 , HOH D:460binding site for residue EDO D 308
33AF6SOFTWAREASN D:249 , ASP D:254 , HOH D:414 , HOH D:627binding site for residue EDO D 309

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:203 -A:258
2B:203 -B:258
3C:203 -C:258
4D:203 -D:258

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Ser A:11 -Pro A:12
2Glu A:163 -Pro A:164
3Lys A:201 -Pro A:202
4Ser B:11 -Pro B:12
5Glu B:163 -Pro B:164
6Lys B:201 -Pro B:202
7Ser C:11 -Pro C:12
8Glu C:163 -Pro C:164
9Lys C:201 -Pro C:202
10Ser D:11 -Pro D:12
11Glu D:163 -Pro D:164
12Lys D:201 -Pro D:202

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5CBS)

(-) 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....eee....hhhhhhhhh..hhhhhhhhhhhhhh.......hhhhhhhhhhhh...eeeeeehhhhhhhhh.....eeee......eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cbs A   1 KTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKGTPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLNEQGLLDKLKNKWWYDKGECGS 260
                                    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: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....eee....hhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhh...eeeeeehhhhhhhhh.....eeee......eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cbs B   2 TVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKGTPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLNEQGLLDKLKNKWWYDKGECGS 260
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251         


Chain C from PDB  Type:PROTEIN  Length:261
                                                                                                                                                                                                                                                                                                     
               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....hhhhhhhhh..hhhhhhhhhhhhhh.......hhhhhhhhhhhh...eeeeeehhhhhhhhh.....eeee......eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cbs C  -1 ANKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKGTPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLNEQGLLDKLKNKWWYDKGECG 259
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258 


Chain D from PDB  Type:PROTEIN  Length:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.......ee..hhhhhhhhh.eehhhhhhhhhhhhhhh..eeeee................hhhhhhhhh....ee......hhhhhhheee....eee.eeeeee......hhhhhhh....eee....hhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhh...eeeeeehhhhhhhh......eeee......eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cbs D  -2 GANKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKGTPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLNEQGLLDKLKNKWWYDKGECG 259
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257
   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 5CBS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (49, 49)

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(-) 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 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

(no "Related Entries Specified in the PDB File" available for 5CBS)