Research workbench
Crystal structure of the NI(II)(CHRO)2-D(TTGGGCCGAA/TTCGGCCCAA) complex at 2.94 ångström resolution
Analyse Crystal structure of the NI(II)(CHRO)2-D(TTGGGCCGAA/TTCGGCCCAA) complex at 2.94… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L76
- Type
- DNA
- Length
- 39 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*TP*TP*GP*GP*GP*CP*CP*GP*AP*A)-3'); DNA (5'-D(*TP*TP*CP*GP*GP*CP*CP*CP*AP*A)-3')
- Ligands
- CDR, ARI, 1GL, ERI, CPH, NI
Structure
x-ray diffraction · 3 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | DNA (5'-D(*TP*TP*GP*GP*GP*CP*CP*GP*AP*A)-3') | dna | 10 | — | — |
| B | DNA (5'-D(*TP*TP*CP*GP*GP*CP*CP*CP*AP*A)-3') | dna | 10 | — | — |
| C | DNA (5'-D(*TP*TP*CP*GP*GP*CP*CP*CP*AP*A)-3') | dna | 9 | — | — |
Ligands and binding sites
- CDR · (2R,5S,6R)-6-methyltetrahydro-2H-pyran-2,5-diol · ligand · 8 copies · chains B, A, C, D
- ARI · (2R,3R,6R)-6-hydroxy-2-methyltetrahydro-2H-pyran-3-yl acetate · ligand · 4 copies · chains A, B, C, D
- 1GL · 2,6-dideoxy-4-O-methyl-alpha-D-galactopyranose · ligand · 4 copies · chains A, B, C, D
- ERI · 3-C-methyl-4-O-acetyl-alpha-L-Olivopyranose · ligand · 4 copies · chains A, B, C, D
- CPH · (1S)-5-deoxy-1-O-methyl-1-C-[(2R,3S)-3,5,7,10-tetrahydroxy-6-methyl-4-oxo-1,2,3,4-tetrahydroanthracen-2-yl]-D-xylulose · ligand · 4 copies · chains A, B, C, D
- NI · Nickel (II) ion · metal · 7 copies · chains B, A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
2 interfaces between chains.
- A–B · 466 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- C–D · 384 Ų buried · 40 hydrogen bonds · nucleic-nucleic
Compared structures
- 6L76 · Crystal structure of the Ni(II)(Chro)2-d(TTGGGCCGAA/TTCGGCCCAA) complex at 2.94 angstrom… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 6L76 · PDBe 6L76
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