Research workbench
CALCIUM(II) and COPPER(II) bound to the Z-DNA form of D(CGCGCG), complexed by chloride and mes
Analyse CALCIUM(II) and COPPER(II) bound to the Z-DNA form of D(CGCGCG), complexed by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XQZ
- Type
- DNA
- Length
- 48 nucleotides
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
- Ligands
- CU, CA, CL
- Pockets
- 1 · best druggability 0.34
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | DNA (5'-D(*CP*GP*CP*GP*CP*G)-3') | dna | 6 | — | — |
Ligands and binding sites
- CU · Copper (II) ion · metal · 6 copies · chains A, D, B, C, E, H, F, G
- CA · Calcium ion · metal · 2 copies · chains A, H, E
- CL · Chloride ion · ion · 7 copies · chains A, B, D, C, F, G, H, E
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, D
- MOH · Methanol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.34 | 0.74 | 19 | CL, MES |
Interfaces
12 interfaces between chains.
- E–F · 325 Ų buried · 33 hydrogen bonds · nucleic-nucleic
- A–B · 318 Ų buried · 24 hydrogen bonds · nucleic-nucleic
- C–D · 315 Ų buried · 25 hydrogen bonds · nucleic-nucleic
- G–H · 313 Ų buried · 24 hydrogen bonds · nucleic-nucleic
- F–H · 156 Ų buried · 2 hydrogen bonds · nucleic-nucleic
Compared structures
- 4XQZ · Calcium(II) and copper(II) bound to the Z-DNA form of d(CGCGCG), complexed by chloride… · 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 4XQZ · PDBe 4XQZ
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