Research workbench
Structure of [CO2+-(chromomycin A3)2]-D(TTGGCGAA)2 complex
Analyse Structure of [CO2+-(chromomycin A3)2]-D(TTGGCGAA)2 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6J0I
- Type
- DNA
- Length
- 48 nucleotides
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*TP*TP*GP*GP*CP*GP*AP*A)-3')
- Ligands
- CDR, ARI, 1GL, ERI, CRH, CO
- Pockets
- 2 · best druggability 0.23
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | DNA (5'-D(*TP*TP*GP*GP*CP*GP*AP*A)-3') | dna | 8 | — | — |
Ligands and binding sites
- CDR · (2R,5S,6R)-6-methyltetrahydro-2H-pyran-2,5-diol · ligand · 12 copies · chains A, B, C, D, E, F
- ARI · (2R,3R,6R)-6-hydroxy-2-methyltetrahydro-2H-pyran-3-yl acetate · ligand · 6 copies · chains A, B, C, D, E, F
- 1GL · 2,6-dideoxy-4-O-methyl-alpha-D-galactopyranose · ligand · 6 copies · chains A, B, C, D, E, F
- ERI · 3-C-methyl-4-O-acetyl-alpha-L-Olivopyranose · ligand · 6 copies · chains A, B, C, D, E, F
- CRH · 1,2-hydro-1-oxy-3,4-hydro-3-(1-methoxy-2-oxy-3,4-dihydroxypentyl)-8,9-dihyroxy-7-methylanthracene · ligand · 6 copies · chains A, B, C, D, E, F
- CO · Cobalt (II) ion · metal · 7 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.23 | 0.72 | 8 | empty |
| 2 | 54 | 0.22 | 0.71 | 9 | empty |
Interfaces
11 interfaces between chains.
- E–F · 380 Ų buried · 41 hydrogen bonds · nucleic-nucleic
- A–B · 375 Ų buried · 41 hydrogen bonds · nucleic-nucleic
- C–D · 372 Ų buried · 29 hydrogen bonds · nucleic-nucleic
- C–E · 106 Ų buried · 4 hydrogen bonds · nucleic-nucleic
- B–D · 105 Ų buried · 2 hydrogen bonds · nucleic-nucleic
Compared structures
- 6J0I · Structure of [Co2+-(Chromomycin A3)2]-d(TTGGCGAA)2 complex · the same entry in another collection · chain B against B, 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 6J0I · PDBe 6J0I
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