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(-) Description

Title :  CRYSTAL STRUCTURE OF THE THERMOTOGA MARITIMA LYSINE RIBOSWITCH BOUND TO LYSINE
 
Authors :  A. A. Serganov
Date :  20 Jun 08  (Deposition) - 16 Sep 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Riboswitch, Lysine, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Serganov, L. Huang, D. J. Patel
Structural Insights Into Amino Acid Binding And Gene Contro By A Lysine Riboswitch.
Nature V. 455 1263 2008
PubMed-ID: 18784651  |  Reference-DOI: 10.1038/NATURE07326

(-) Compounds

Molecule 1 - RNA (174-MER)
    Chains: A
    Engineered: YES
    Other Details: IN VITRO TRANSCRIBED RNA FROM THE LEADER REGION OF THE THERMATOGA MARITIMA MSB8 ASD GENE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 39)

Asymmetric/Biological Unit (7, 39)
No.NameCountTypeFull Name
11PE3Ligand/IonPENTAETHYLENE GLYCOL
2CCC1Mod. NucleotideCYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
3IPA1Ligand/IonISOPROPYL ALCOHOL
4K3Ligand/IonPOTASSIUM ION
5LYS1Ligand/IonLYSINE
6MG1Ligand/IonMAGNESIUM ION
7NA29Ligand/IonSODIUM ION

(-) Sites  (35, 35)

Asymmetric Unit (35, 35)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:853 , HOH A:977BINDING SITE FOR RESIDUE LYS A 175
02AC2SOFTWARELYS A:175 , HOH A:797 , HOH A:887BINDING SITE FOR RESIDUE K A 200
03AC3SOFTWAREHOH A:367 , HOH A:368 , HOH A:407 , HOH A:862 , HOH A:1032BINDING SITE FOR RESIDUE NA A 812
04AC4SOFTWAREHOH A:367 , HOH A:368 , HOH A:369 , HOH A:375BINDING SITE FOR RESIDUE NA A 201
05AC5SOFTWAREHOH A:793 , HOH A:864 , HOH A:907 , HOH A:944BINDING SITE FOR RESIDUE NA A 202
06AC6SOFTWAREHOH A:414 , HOH A:561 , HOH A:637 , HOH A:682 , HOH A:1201 , HOH A:1202BINDING SITE FOR RESIDUE NA A 203
07AC7SOFTWAREHOH A:1203 , HOH A:1204 , HOH A:1205 , HOH A:1206BINDING SITE FOR RESIDUE NA A 204
08AC8SOFTWAREHOH A:1207 , HOH A:1208 , HOH A:1209 , HOH A:1210 , HOH A:1211 , HOH A:1212BINDING SITE FOR RESIDUE NA A 205
09AC9SOFTWAREHOH A:1209 , HOH A:1212 , HOH A:1213 , HOH A:1214 , HOH A:1216BINDING SITE FOR RESIDUE NA A 206
10BC1SOFTWAREHOH A:1215 , HOH A:1216 , HOH A:1217 , HOH A:1218 , HOH A:1219 , HOH A:1220BINDING SITE FOR RESIDUE NA A 207
11BC2SOFTWAREHOH A:1221 , HOH A:1222 , HOH A:1223 , HOH A:1224 , HOH A:1225 , HOH A:1226BINDING SITE FOR RESIDUE NA A 208
12BC3SOFTWAREHOH A:1222 , HOH A:1223 , HOH A:1225 , HOH A:1227 , HOH A:1228BINDING SITE FOR RESIDUE NA A 209
13BC4SOFTWAREHOH A:1229 , HOH A:1230 , HOH A:1231BINDING SITE FOR RESIDUE NA A 210
14BC5SOFTWAREHOH A:1232 , HOH A:1233 , HOH A:1234 , HOH A:1235 , HOH A:1236BINDING SITE FOR RESIDUE NA A 211
15BC6SOFTWAREHOH A:415 , HOH A:426 , HOH A:561 , HOH A:682 , HOH A:1047 , HOH A:1201BINDING SITE FOR RESIDUE NA A 212
16BC7SOFTWAREHOH A:527 , HOH A:798 , HOH A:799 , HOH A:885 , HOH A:1221 , HOH A:1226BINDING SITE FOR RESIDUE NA A 213
17BC8SOFTWAREHOH A:317 , HOH A:319 , HOH A:627 , HOH A:653 , HOH A:744BINDING SITE FOR RESIDUE NA A 214
18BC9SOFTWAREHOH A:408 , HOH A:918 , HOH A:969BINDING SITE FOR RESIDUE NA A 215
19CC1SOFTWAREHOH A:328 , HOH A:753 , HOH A:809 , HOH A:872BINDING SITE FOR RESIDUE NA A 216
20CC2SOFTWAREHOH A:347 , HOH A:376 , HOH A:642 , HOH A:858 , HOH A:952BINDING SITE FOR RESIDUE NA A 217
21CC3SOFTWAREHOH A:321 , HOH A:808 , HOH A:811 , HOH A:942 , HOH A:989BINDING SITE FOR RESIDUE NA A 218
22CC4SOFTWAREHOH A:405 , HOH A:488 , HOH A:634 , HOH A:947 , HOH A:1025 , HOH A:1045BINDING SITE FOR RESIDUE NA A 219
23CC5SOFTWAREHOH A:328 , HOH A:706 , HOH A:753 , HOH A:870BINDING SITE FOR RESIDUE NA A 220
24CC6SOFTWAREHOH A:721 , HOH A:808 , HOH A:816 , HOH A:867 , HOH A:942 , HOH A:989BINDING SITE FOR RESIDUE NA A 221
25CC7SOFTWAREHOH A:457 , HOH A:669 , HOH A:674 , HOH A:1003BINDING SITE FOR RESIDUE NA A 222
26CC8SOFTWAREHOH A:346 , HOH A:622 , HOH A:832BINDING SITE FOR RESIDUE NA A 223
27CC9SOFTWAREHOH A:599 , HOH A:809 , HOH A:872 , HOH A:1239BINDING SITE FOR RESIDUE NA A 224
28DC1SOFTWAREHOH A:498 , HOH A:636BINDING SITE FOR RESIDUE NA A 225
29DC2SOFTWAREHOH A:456 , HOH A:990 , HOH A:996 , HOH A:1027 , HOH A:1044BINDING SITE FOR RESIDUE NA A 226
30DC3SOFTWAREHOH A:309 , HOH A:355 , HOH A:359 , HOH A:377 , HOH A:393 , HOH A:825BINDING SITE FOR RESIDUE NA A 227
31DC4SOFTWAREHOH A:427 , HOH A:439 , HOH A:546 , HOH A:624 , HOH A:644BINDING SITE FOR RESIDUE NA A 228
32DC5SOFTWAREHOH A:1240 , HOH A:1241 , HOH A:1242 , HOH A:1243 , HOH A:1244BINDING SITE FOR RESIDUE MG A 229
33DC6SOFTWAREHOH A:315 , HOH A:925 , HOH A:1045 , HOH A:1235 , HOH A:1236BINDING SITE FOR RESIDUE K A 230
34DC7SOFTWAREHOH A:456 , HOH A:689 , HOH A:792 , HOH A:1027BINDING SITE FOR RESIDUE K A 231
35DC8SOFTWAREHOH A:902 , HOH A:967BINDING SITE FOR RESIDUE 1PE A 250

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DIL)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3DIL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 3DIL)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
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Chain A from PDB  Type:RNA  Length:174
                                                                                                                                                                                                              
                 3dil A   1 GGCCGACGGAGGCGCGCCCGAGAUGAGUAGGCUGUCCCAUCAGGGGAGGAAUCGGGGACGGCUGAAAGGCGAGGGCGCCGAAGGGUGCAGAGUUCCUCCCGCUCUGCAUGCCUGGGGGUAUGGGGAAUACCCAUACCACUGUCACGGAGGUCUCUCCGUGGAGAGCCGUCGGUc 174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   |
                                                                                                                                                                                                       174-CCC
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

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(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

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3dig 3dim 3dio 3diq 3dir 3dis 3dix 3diy 3diz 3dj0 3dj2