4U6K - JenaLib

Title :   CRYSTAL STRUCTURE OF DNA/RNA DUPLEX CONTAINING 2'-4'-BNA-NC

Authors :   J. Kondo, Y. Nomura, Y. Kitahara, S. Obika, H. Torigoe

Date :   29 Jul 14 (Deposition) - 19 Aug 15 (Release) - 19 Aug 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Dna/Rna Duplex, Antisense, Bridged Nucleic Acid, Dna-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Kondo, Y. Nomura, Y. Kitahara, S. Obika, H. Torigoe
Crystal Structure Of Dna/Rna Duplex Containing 2', 4'-Bna-Nc
To Be Published
PubMed: search

Compounds

*Molecule 1 - RNA (5'-R(GPAPAPGPAPAPGPAPG)-3')**
	Chains	:	A, C
	Engineered	:	YES
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630
	Synthetic	:	YES

*Molecule 2 - DNA (5'-D((NCU)P(NTT)PCPTPTPCPTP(NTT)P(NCU))-3')**
	Chains	:	B, D
	Engineered	:	YES
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630
	Synthetic	:	YES

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 11)

Asymmetric Unit (3, 11)

No.	Name	Count	Type	Full Name
1	NCO	3	Ligand/Ion	COBALT HEXAMMINE(III)
2	NCU	4	Mod. Nucleotide	[(1R,5R,7R,8S)-7-(4-AMINO-5-METHYL-2-OXOPYRIMIDIN-1(2H)-YL)-8-HYDROXY-3-METHYL-2,6-DIOXA-3-AZABICYCLO[3.2.1]OCT-5-YL]METHYL DIHYDROGEN PHOSPHATE
3	NTT	4	Mod. Nucleotide	[(1R,5R,7R,8S)-8-HYDROXY-3-METHYL-7-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-2,6-DIOXA-3-AZABICYCLO[3.2.1]OCT-5-YL]METHYL DIHYDROGEN PHOSPHATE

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	NCO	2	Ligand/Ion	COBALT HEXAMMINE(III)
2	NCU	2	Mod. Nucleotide	[(1R,5R,7R,8S)-7-(4-AMINO-5-METHYL-2-OXOPYRIMIDIN-1(2H)-YL)-8-HYDROXY-3-METHYL-2,6-DIOXA-3-AZABICYCLO[3.2.1]OCT-5-YL]METHYL DIHYDROGEN PHOSPHATE
3	NTT	2	Mod. Nucleotide	[(1R,5R,7R,8S)-8-HYDROXY-3-METHYL-7-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-2,6-DIOXA-3-AZABICYCLO[3.2.1]OCT-5-YL]METHYL DIHYDROGEN PHOSPHATE

Biological Unit 2 (3, 5)

No.	Name	Count	Type	Full Name
1	NCO	1	Ligand/Ion	COBALT HEXAMMINE(III)
2	NCU	2	Mod. Nucleotide	[(1R,5R,7R,8S)-7-(4-AMINO-5-METHYL-2-OXOPYRIMIDIN-1(2H)-YL)-8-HYDROXY-3-METHYL-2,6-DIOXA-3-AZABICYCLO[3.2.1]OCT-5-YL]METHYL DIHYDROGEN PHOSPHATE
3	NTT	2	Mod. Nucleotide	[(1R,5R,7R,8S)-8-HYDROXY-3-METHYL-7-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-2,6-DIOXA-3-AZABICYCLO[3.2.1]OCT-5-YL]METHYL DIHYDROGEN PHOSPHATE

Sites (9, 9)

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	A A:3 , G A:4 , HOH A:233 , HOH A:261 , HOH A:262 , HOH A:264	binding site for residue NCO A 101
2	AC2	SOFTWARE	A A:8 , G A:9 , HOH A:209 , NCU B:1 , A C:8 , G C:9 , HOH C:205 , HOH C:228	binding site for residue NCO A 102
3	AC3	SOFTWARE	A C:3 , G C:4 , HOH C:226 , HOH C:231 , HOH C:249 , HOH C:253 , HOH C:254	binding site for residue NCO C 101
4	AC4	SOFTWARE	A A:2 , A A:8 , G A:9 , NCO A:102 , DC B:3 , NTT B:8 , NCU B:9 , HOH B:109 , HOH B:113 , HOH B:115 , HOH B:116 , HOH B:121 , HOH B:136 , HOH B:140 , HOH B:146 , G C:9 , NCU D:1 , HOH D:128	binding site for residues NCU B 1 and NTT B 2
5	AC5	SOFTWARE	G A:1 , A A:2 , A A:3 , G A:9 , NCU B:1 , NTT B:2 , DT B:7 , HOH B:103 , HOH B:104 , HOH B:110 , HOH B:114 , HOH B:117 , HOH B:123 , HOH B:130 , HOH B:133 , HOH B:135 , HOH B:137 , HOH B:138 , HOH B:139 , HOH B:144 , G C:1 , NCU D:1 , HOH D:113	binding site for residues NTT B 8 and NCU B 9
6	AC6	SOFTWARE	G A:9 , NCU B:1 , NCU B:9 , A C:8 , G C:9 , HOH C:215 , DC D:3 , HOH D:113 , HOH D:115 , HOH D:116 , HOH D:120 , HOH D:125 , HOH D:128 , HOH D:137	binding site for residues NCU D 1 and NTT D 2
7	AC7	SOFTWARE	G C:7 , A C:8 , G C:9 , NCU D:1 , DT D:4 , HOH D:108 , HOH D:109 , HOH D:115 , HOH D:116 , HOH D:120 , HOH D:125 , HOH D:126 , HOH D:133 , HOH D:137 , HOH D:142	binding site for Di-nucleotide NTT D 2 and DC D 3
8	AC8	SOFTWARE	A C:2 , A C:3 , G C:4 , DC D:6 , NCU D:9 , HOH D:102 , HOH D:111 , HOH D:112 , HOH D:121 , HOH D:122 , HOH D:124 , HOH D:130	binding site for Di-nucleotide DT D 7 and NTT D 8
9	AC9	SOFTWARE	G A:1 , G C:1 , A C:2 , A C:3 , DT D:7 , HOH D:101 , HOH D:102 , HOH D:106 , HOH D:107 , HOH D:111 , HOH D:114 , HOH D:119 , HOH D:121 , HOH D:122 , HOH D:129 , HOH D:130 , HOH D:132 , HOH D:134 , HOH D:139	binding site for residues NTT D 8 and NCU D 9

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

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Chain A from PDB  Type:RNA  Length:9
                                       
                   4u6k A 1 GAAGAAGAG 9

Chain B from PDB  Type:DNA/RNA  Length:9
                                       
                   4u6k B 1 xxCTTCTxx 9
                            ||     ||
                            1-NCU  8-NTT
                             2-NTT  9-NCU

Chain C from PDB  Type:RNA  Length:9
                                       
                   4u6k C 1 GAAGAAGAG 9

Chain D from PDB  Type:DNA/RNA  Length:9
                                       
                   4u6k D 1 xxCTTCTxx 9
                            ||     ||
                            1-NCU  8-NTT
                             2-NTT  9-NCU

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Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

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