5DDR - JenaLib

Title :   L-GLUTAMINE RIBOSWITCH BOUND WITH L-GLUTAMINE SOAKED WITH CS+

Authors :   A. Ren, D. J. Patel

Date :   25 Aug 15 (Deposition) - 23 Dec 15 (Release) - 05 Apr 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.61

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

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 31)

Sites (31, 31)

Asymmetric Unit (31, 31)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	C A:1 , G A:22 , G A:23 , G A:54 , C A:58 , G A:59 , C A:60 , MG A:107 , HOH A:201 , HOH A:254	binding site for residue GLN A 101
02	AC2	SOFTWARE	MG A:109 , HOH A:208 , HOH A:282	binding site for residue K A 102
03	AC3	SOFTWARE	CS A:113 , HOH A:206 , HOH A:208 , HOH A:282	binding site for residue K A 103
04	AC4	SOFTWARE	HOH B:206 , HOH B:286 , HOH B:290	binding site for residue K A 104
05	AC5	SOFTWARE	G A:30 , G A:31 , U A:32 , HOH A:240 , HOH A:249 , HOH A:259 , HOH A:293	binding site for residue K A 105
06	AC6	SOFTWARE	HOH A:217 , HOH A:219 , HOH A:264 , HOH A:265 , HOH A:305 , HOH A:310	binding site for residue MG A 106
07	AC7	SOFTWARE	G A:54 , GLN A:101 , HOH A:201 , HOH A:210 , HOH A:225 , HOH A:245 , HOH A:254	binding site for residue MG A 107
08	AC8	SOFTWARE	HOH A:247 , HOH A:258 , HOH A:276 , HOH A:289 , HOH A:307	binding site for residue MG A 108
09	AC9	SOFTWARE	K A:102 , HOH A:246 , HOH A:248 , HOH A:251 , HOH A:277 , HOH A:282 , HOH A:297 , HOH A:304	binding site for residue MG A 109
10	AD1	SOFTWARE	A A:29 , HOH A:218 , HOH A:242 , HOH A:253 , HOH A:286 , HOH A:309	binding site for residue MG A 110
11	AD2	SOFTWARE	HOH A:243 , HOH A:288 , HOH A:295 , HOH A:302 , HOH A:303	binding site for residue MG A 111
12	AD3	SOFTWARE	G A:11 , G A:12 , HOH A:213 , HOH A:238 , HOH A:268 , HOH A:276 , HOH A:298	binding site for residue CS A 112
13	AD4	SOFTWARE	G A:20 , C A:21 , K A:103 , HOH A:206 , HOH A:223 , HOH A:272	binding site for residue CS A 113
14	AD5	SOFTWARE	G A:46 , HOH A:255 , HOH A:259 , HOH A:284	binding site for residue CS A 114
15	AD6	SOFTWARE	C B:1 , G B:22 , G B:23 , G B:54 , C B:58 , G B:59 , C B:60 , MG B:106 , HOH B:205 , HOH B:212 , HOH B:223 , HOH B:238	binding site for residue GLN B 101
16	AD7	SOFTWARE	A A:13 , HOH A:202 , C B:33	binding site for residue K B 102
17	AD8	SOFTWARE	U B:32 , G B:46 , K B:104 , HOH B:257 , HOH B:279 , HOH B:303 , HOH B:310	binding site for residue K B 103
18	AD9	SOFTWARE	G B:30 , G B:31 , U B:32 , K B:103 , HOH B:285 , HOH B:303	binding site for residue K B 104
19	AE1	SOFTWARE	C B:16 , HOH B:292 , HOH B:293	binding site for residue MG B 105
20	AE2	SOFTWARE	G B:54 , GLN B:101 , HOH B:205 , HOH B:212 , HOH B:221 , HOH B:223 , HOH B:231	binding site for residue MG B 106
21	AE3	SOFTWARE	G B:12 , A B:14 , HOH B:228 , HOH B:249 , HOH B:254 , HOH B:309	binding site for residue MG B 107
22	AE4	SOFTWARE	G B:18 , HOH B:202 , HOH B:269 , HOH B:283 , HOH B:288 , HOH B:311	binding site for residue MG B 108
23	AE5	SOFTWARE	G B:51 , HOH B:284 , HOH B:298	binding site for residue NA B 109
24	AE6	SOFTWARE	A B:25 , G B:26 , HOH B:235 , HOH B:273 , HOH B:282	binding site for residue NA B 110
25	AE7	SOFTWARE	A B:25 , G B:26 , HOH B:235 , HOH B:270 , HOH B:282	binding site for residue NA B 111
26	AE8	SOFTWARE	G B:26 , G B:51 , HOH B:284	binding site for residue NA B 112
27	AE9	SOFTWARE	HOH B:209 , HOH B:250	binding site for residue CS B 113
28	AF1	SOFTWARE	HOH B:232 , HOH B:266	binding site for residue CS B 114
29	AF2	SOFTWARE	G B:11	binding site for residue CS B 115
30	AF3	SOFTWARE	G B:12	binding site for residue CS B 116
31	AF4	SOFTWARE	LYS C:19 , LYS C:79 , HOH C:214	binding site for residue MG C 101

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

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

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

Chain C 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.........eeee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                  5ddr C  2 VPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAK 95
                                    11        21        31        41        51        61        71        81        91

Chain D from PDB  Type:PROTEIN  Length:94
                                                                                                                             
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee......hhhhhhhhhhhhhhh...eeeee..........eeeee.hhhhhhhhhhhhh..ee..ee.eeee.....hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                  5ddr D  4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMK 97
                                    13        23        33        43        53        63        73        83        93

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

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Gene Ontology (17, 17)

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