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(-) Description

Title :  STRUCTURE OF THE STANDARD KINK TURN HMKT-7 AS STEM LOOP IN P212121 SPACE GROUP
 
Authors :  L. Huang, D. M. J. Lilley
Date :  05 Oct 15  (Deposition) - 25 May 16  (Release) - 06 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,E  (1x)
Biol. Unit 2:  D,F,G,H  (1x)
Keywords :  Rna, Kink Turn, Rna Motif (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Huang, J. Wang, D. M. J. Lilley
A Critical Base Pair In K-Turns Determines The Conformational Class Adopted, And Correlates With Biological Function.
Nucleic Acids Res. V. 44 5390 2016
PubMed-ID: 27016741  |  Reference-DOI: 10.1093/NAR/GKW201

(-) Compounds

Molecule 1 - HMKT-7
    Chains: A, B, C, D, E, F, G, H
    Fragment: KINK TURN MOTIF, RESIDUES 1-24
    Organism Scientific: HALOARCULA MARISMORTUI
    Organism Taxid: 2238
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): ABC E   
Biological Unit 2 (1x):    D FGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 24)

Asymmetric Unit (2, 24)
No.NameCountTypeFull Name
1MG21Ligand/IonMAGNESIUM ION
2NA3Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2NA-1Ligand/IonSODIUM ION

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREG A:3 , G A:4 , G A:5 , MG A:1026 , HOH A:2001BINDING SITE FOR RESIDUE MG A1025
02AC2SOFTWAREG A:2 , G A:3 , G A:4 , MG A:1025BINDING SITE FOR RESIDUE MG A1026
03AC3SOFTWAREG A:5 , G A:20BINDING SITE FOR RESIDUE MG A1027
04AC4SOFTWAREG F:4 , G F:5 , MG F:1026BINDING SITE FOR RESIDUE MG F1025
05AC5SOFTWAREG F:5 , MG F:1025BINDING SITE FOR RESIDUE MG F1026
06AC6SOFTWAREG F:10BINDING SITE FOR RESIDUE MG F1027
07AC7SOFTWAREG C:20BINDING SITE FOR RESIDUE MG C1025
08AC8SOFTWAREG D:10BINDING SITE FOR RESIDUE MG D1025
09AC9SOFTWAREG C:10BINDING SITE FOR RESIDUE MG C1026
10BC1SOFTWAREG B:2 , G B:3 , HOH B:2001BINDING SITE FOR RESIDUE MG B1025
11BC2SOFTWAREG B:3 , G B:4 , G B:5 , MG B:1027BINDING SITE FOR RESIDUE MG B1026
12BC3SOFTWAREG B:5 , MG B:1026 , HOH B:2002BINDING SITE FOR RESIDUE MG B1027
13BC4SOFTWAREG B:5BINDING SITE FOR RESIDUE MG B1028
14BC5SOFTWAREG E:10BINDING SITE FOR RESIDUE MG E1025
15BC6SOFTWAREG C:4 , G C:5BINDING SITE FOR RESIDUE MG C1027
16BC7SOFTWAREG B:10BINDING SITE FOR RESIDUE MG B1029
17BC8SOFTWAREG G:3 , G G:4 , G G:5BINDING SITE FOR RESIDUE MG G1025
18BC9SOFTWAREG A:10BINDING SITE FOR RESIDUE MG A1028
19CC1SOFTWAREG E:5 , G E:20BINDING SITE FOR RESIDUE MG E1026
20CC2SOFTWAREG E:5BINDING SITE FOR RESIDUE MG E1027
21CC3SOFTWAREG E:3 , G E:4 , G E:5BINDING SITE FOR RESIDUE MG E1028
22CC4SOFTWAREA D:19 , G F:14BINDING SITE FOR RESIDUE NA F1028
23CC5SOFTWAREA A:19 , G E:14BINDING SITE FOR RESIDUE NA A1029
24CC6SOFTWAREG A:14 , A E:19BINDING SITE FOR RESIDUE NA A1030

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FJ1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5FJ1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FJ1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FJ1)

(-) Exons   (0, 0)

(no "Exon" information available for 5FJ1)

(-) 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:24
                                                       
                  5fj1 A  1 UGGGGAGCCGAAAGGCGAAGAACC 24
                                    10        20    


Chain B from PDB  Type:RNA  Length:24
                                                       
                  5fj1 B  1 UGGGGAGCCGAAAGGCGAAGAACC 24
                                    10        20    


Chain C from PDB  Type:RNA  Length:24
                                                       
                  5fj1 C  1 UGGGGAGCCGAAAGGCGAAGAACC 24
                                    10        20    


Chain D from PDB  Type:RNA  Length:24
                                                       
                  5fj1 D  1 UGGGGAGCCGAAAGGCGAAGAACC 24
                                    10        20    


Chain E from PDB  Type:RNA  Length:24
                                                       
                  5fj1 E  1 UGGGGAGCCGAAAGGCGAAGAACC 24
                                    10        20    


Chain F from PDB  Type:RNA  Length:24
                                                       
                  5fj1 F  1 UGGGGAGCCGAAAGGCGAAGAACC 24
                                    10        20    


Chain G from PDB  Type:RNA  Length:24
                                                       
                  5fj1 G  1 UGGGGAGCCGAAAGGCGAAGAACC 24
                                    10        20    


Chain H from PDB  Type:RNA  Length:24
                                                       
                  5fj1 H  1 UGGGGAGCCGAAAGGCGAAGAACC 24
                                    10        20
   Legend:   → Mismatch (orange background)
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  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 5FJ1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FJ1)

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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 Related Entries

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(-) Related Entries Specified in the PDB File

5fj0 STRUCTURE OF THE STANDARD KINK TURN HMKT-7 AS SIMPLE DUPLEX IN P4222 SPACE GROUP
5fj4 STRUCTURE OF THE STANDARD KINK TURN HMKT-7 AS STEM LOOP BOUND WITH U1A AND L7AE PROTEINS
5fjc SAM-I RIBOSWITCH BEARING THE H. MARISMORTUI KT-7 VARIANT C-2BU