MolNFT v2 · #117058 · protein + DNA
Nucleosome core particle containing adducts of gold(I)-triethylphosphane and ruthenium(II)-toluene PTA complexes
5DNN: “Nucleosome core particle containing adducts of gold(I)-triethylphosphane and ruthenium(II)-toluene PTA…”. X-ray diffraction at 2.8, 4 ligands (AUF, RAX, MG). MolNFT v2 #117058 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5DNN
- Type
- protein + DNA
- Length
- 1,055 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Xenopus laevis; SYNTHETIC CONSTRUCT
- UniProt
- P84233, P62799, Q6AZJ8, P02281
- Ligands
- AUF, RAX, MG, SO4
Structure
x-ray diffraction · resolution 2.8 · 7 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | — | protein | 97 | — | P84233 |
| B | — | protein | 82 | — | P62799 |
| C, G | — | protein | 106 | — | Q6AZJ8 |
| D, H | — | protein | 95 | — | P02281 |
| F | — | protein | 87 | — | P62799 |
| I | — | dna | 145 | — | — |
| J | — | dna | 145 | — | — |
Ligands and binding sites
- AUF · triethylphosphanuidylgold(1+) · ligand · 2 copies · chains A, E
- RAX · dichloro[(1,2,3,4,5,6-eta)-6-methylbenzene]1,3,5-triaza-7lambda~5~-phosphatricyclo[3.3.1.1~3,7~]dec-7-ylruthenium · ligand · 2 copies · chains G, H
- MG · Magnesium ion · metal · chains E
- SO4 · Sulfate ion · ion · 3 copies · chains C, D, J, G, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 5DNN · Nucleosome core particle containing adducts of GOLD(I)- triethylphosphane and… · the same entry in another collection · chain J against J, TM-score 1.00
- P84233 · AlphaFold monomer V2.0 prediction for histone H3.2 (P84233) · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P84233
- Every structure of UniProt P62799
- Every structure of UniProt Q6AZJ8
- Every structure of UniProt P02281
- Elsewhere: RCSB PDB 5DNN · PDBe 5DNN · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281
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