Research workbench
X-ray structure of NCP145 with CHLORIDO(ETA-6-P-CYMENE)(N- fluorophenyl-2-PYRIDINECARBOTHIOAMIDE)OSMIUM(II)
Analyse X-ray structure of NCP145 with CHLORIDO(ETA-6-P-CYMENE)(N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J8W
- Type
- protein + DNA
- Length
- 1,055 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.2; Histone H4; Histone H2A; Histone H2B 1.1; DNA (145-mer)
- UniProt
- P84233, P62799, Q6AZJ8, P02281
- Ligands
- 1MK, MG, SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 7 distinct chains · 63% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3.2 | protein | 97 | 66% helix, 4% strand | P84233 |
| B | Histone H4 | protein | 82 | 61% helix, 9% strand | P62799 |
| C, G | Histone H2A | protein | 106 | 56% helix, 7% strand | Q6AZJ8 |
| D, H | Histone H2B 1.1 | protein | 95 | 74% helix, 4% strand | P02281 |
| F | Histone H4 | protein | 87 | 59% helix, 8% strand | P62799 |
| I | DNA (145-mer) | dna | 145 | — | — |
| J | DNA (145-mer) | dna | 145 | — | — |
Ligands and binding sites
- 1MK · chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)osmium(II) · ligand · 3 copies · chains B, D, G, H, C, F
- MG · Magnesium ion · metal · chains E, F
- 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.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1131 | 0.82 | 0.83 | 122 | 1MK |
| 2 | 350 | 0.74 | 0.86 | 50 | empty |
| 3 | 945 | 0.74 | 0.78 | 69 | empty |
| 4 | 319 | 0.74 | 0.86 | 41 | empty |
| 5 | 689 | 0.72 | 0.79 | 70 | empty |
Interfaces
37 interfaces between chains.
- I–J · 6461 Ų buried · 569 hydrogen bonds · nucleic-nucleic
- C–D · 2649 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 2635 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 2601 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 2557 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 4J8W · X-ray structure of NCP145 with chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothio… · 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
- Every structure of UniProt P84233
- Every structure of UniProt P62799
- Every structure of UniProt Q6AZJ8
- Every structure of UniProt P02281
- Elsewhere: RCSB PDB 4J8W · PDBe 4J8W · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281
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