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(-) Description

Title :  L-GLUTAMINE RIBOSWITCH BOUND WITH L-GLUTAMINE
 
Authors :  A. Ren, D. J. Patel
Date :  25 Aug 15  (Deposition) - 23 Dec 15  (Release) - 23 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Riboswitch, L-Glutamine, Bound-Form, Rna, Rna Binding Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Ren, Y. Xue, A. Peselis, A. Serganov, H. M. Al-Hashimi, D. J. Patel
Structural And Dynamic Basis For Low-Affinity, High-Selectivity Binding Of L-Glutamine By The Glutamine Riboswitch.
Cell Rep V. 13 1800 2015
PubMed-ID: 26655897  |  Reference-DOI: 10.1016/J.CELREP.2015.10.062

(-) Compounds

Molecule 1 - RNA (61-MER)
    ChainsA, B
    Organism ScientificSYNECHOCOCCUS ELONGATUS
    Organism Taxid32046
 
Molecule 2 - U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
    ChainsC, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneSNRPA
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymU1A

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A  D
Biological Unit 2 (1x) BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 21)

Asymmetric Unit (3, 21)
No.NameCountTypeFull Name
1GLN2Mod. Amino AcidGLUTAMINE
2MG9Ligand/IonMAGNESIUM ION
3NA10Ligand/IonSODIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GLN1Mod. Amino AcidGLUTAMINE
2MG-1Ligand/IonMAGNESIUM ION
3NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GLN1Mod. Amino AcidGLUTAMINE
2MG-1Ligand/IonMAGNESIUM ION
3NA-1Ligand/IonSODIUM ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREC A:1 , G A:22 , G A:23 , A A:24 , G A:54 , C A:58 , G A:59 , C A:60 , MG A:102 , HOH A:237 , HOH A:241 , HOH A:271 , HOH A:281 , HOH A:285binding site for residue GLN A 101
02AC2SOFTWAREGLN A:101 , HOH A:237 , HOH A:240 , HOH A:241 , HOH A:281 , HOH A:285binding site for residue MG A 102
03AC3SOFTWAREHOH A:218 , HOH A:245 , HOH A:248 , HOH A:269 , HOH A:348 , HOH A:351binding site for residue MG A 103
04AC4SOFTWAREHOH A:220 , HOH A:236 , HOH A:340binding site for residue MG A 104
05AC5SOFTWAREHOH A:255 , HOH A:261 , HOH A:277 , HOH A:332 , HOH A:347 , HOH A:349binding site for residue MG A 105
06AC6SOFTWAREG A:61 , HOH A:203binding site for residue MG A 106
07AC7SOFTWAREG A:11 , G A:12 , HOH A:219 , HOH A:261 , HOH A:320 , HOH A:332binding site for residue NA A 107
08AC8SOFTWAREG A:20 , C A:21 , HOH A:294 , HOH A:314 , HOH A:345binding site for residue NA A 108
09AC9SOFTWAREG A:31 , U A:32 , G A:46 , G A:47 , HOH A:201 , HOH A:264 , HOH A:267binding site for residue NA A 109
10AD1SOFTWAREG A:12 , A A:13 , A A:14 , HOH A:275 , C B:33binding site for residue NA A 110
11AD2SOFTWAREG A:31 , U A:32 , HOH A:264 , HOH A:301 , HOH A:324binding site for residue NA A 111
12AD3SOFTWAREC B:1 , G B:22 , G B:23 , A B:24 , G B:54 , C B:58 , G B:59 , C B:60 , MG B:102 , HOH B:220 , HOH B:237 , HOH B:238 , HOH B:261 , HOH B:263binding site for residue GLN B 101
13AD4SOFTWAREGLN B:101 , HOH B:232 , HOH B:237 , HOH B:238 , HOH B:261 , HOH B:263binding site for residue MG B 102
14AD5SOFTWAREHOH B:211 , HOH B:235 , HOH B:253 , HOH B:304binding site for residue MG B 103
15AD6SOFTWAREHOH B:216 , HOH B:249 , HOH B:275 , HOH B:279 , HOH B:296 , HOH B:301binding site for residue MG B 104
16AD7SOFTWAREHOH B:208 , HOH B:217 , HOH B:289 , HOH B:297 , HOH B:298binding site for residue MG B 105
17AD8SOFTWAREG B:11 , G B:12 , HOH B:208 , HOH B:245 , HOH B:246 , HOH B:265 , HOH B:295binding site for residue NA B 106
18AD9SOFTWAREG B:31 , U B:32 , C B:33 , G B:46 , G B:47 , HOH B:252 , HOH B:254binding site for residue NA B 107
19AE1SOFTWAREG B:19 , G B:20 , C B:21 , HOH B:209 , HOH B:228 , HOH B:293binding site for residue NA B 108
20AE2SOFTWAREC A:33 , HOH A:288 , G B:12 , A B:13 , HOH B:243binding site for residue NA B 109
21AE3SOFTWAREG B:31 , U B:32 , HOH B:239 , HOH B:244 , HOH B:254binding site for residue NA B 110

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DDP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5DDP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DDP)

(-) 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:RNA  Length:61
                                                                                            
                  5ddp A  1 CGUUGACCCAGGAAACUGGGCGGAAGUAAGGUCCAUUGCACUCCGGGCCUGAAGCAACGCG 61
                                    10        20        30        40        50        60 

Chain B from PDB  Type:RNA  Length:61
                                                                                            
                  5ddp B  1 CGUUGACCCAGGAAACUGGGCGGAAGUAAGGUCCAUUGCACUCCGGGCCUGAAGCAACGCG 61
                                    10        20        30        40        50        60 

Chain C from PDB  Type:PROTEIN  Length:93
                                                                                                                            
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee......hhhhhhhhhhhhhhhhh.eeeee..........eeeee.hhhhhhhhhhhhh..ee..ee.eeee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                  5ddp C  3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAK 95
                                    12        22        32        42        52        62        72        82        92   

Chain D from PDB  Type:PROTEIN  Length:94
                                                                                                                             
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee......hhhhhhhhhhhhhhhhh.eeeeee.........eeeee.hhhhhhhhhhhhh..ee..ee.eeee....hhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                  5ddp D  2 VPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAK 95
                                    11        21        31        41        51        61        71        81        91    

   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 5DDP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        SNRPA_HUMAN | P090121aud 1drz 1dz5 1fht 1m5k 1m5o 1m5p 1m5v 1nu4 1oia 1sj3 1sj4 1sjf 1u6b 1urn 1vbx 1vby 1vbz 1vc0 1vc5 1vc6 1zzn 2a3j 2nz4 2oih 2oj3 2u1a 3bo2 3bo3 3bo4 3cul 3cun 3egz 3g8s 3g8t 3g96 3g9c 3hhn 3iin 3irw 3iwn 3k0j 3l3c 3mum 3mur 3mut 3muv 3mxh 3p49 3pgw 3r1h 3r1l 3ucu 3ucz 3ud3 3ud4 3utr 4c4w 4pr6 4prf 4w90 4w92 4yb1 5ddo 5ddq 5ddr 5fj4

(-) Related Entries Specified in the PDB File

5ddo 5ddq 5ddr