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Structure of trptnap-NCP145
Analyse Structure of trptnap-NCP145 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WU8
- Type
- protein + DNA
- Length
- 1,053 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (145-mer); Histone H3.2; Histone H4; Histone H2A type 1; Histone H2B 1.1
- UniProt
- P84233, P62799, P06897, P02281
- Ligands
- CX3, MG, SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 7 distinct chains · 63% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | DNA (145-mer) | dna | 145 | — | — |
| J | DNA (145-mer) | dna | 145 | — | — |
| A, E | Histone H3.2 | protein | 96 | 67% helix, 4% strand | P84233 |
| B | Histone H4 | protein | 82 | 60% helix, 9% strand | P62799 |
| C, G | Histone H2A type 1 | protein | 106 | 56% helix, 7% strand | P06897 |
| D, H | Histone H2B 1.1 | protein | 95 | 74% helix, 4% strand | P02281 |
| F | Histone H4 | protein | 87 | 57% helix, 8% strand | P62799 |
Ligands and binding sites
- CX3 · [2-(3-{bis[2-(amino-kappan)ethyl]amino-kappan}propyl)-1H-benzo[de]isoquinoline-1,3(2H)-dionato(2-) ]platinum(1+) · ligand · 2 copies · chains I, J
- MG · Magnesium ion · metal · chains E, F
- SO4 · Sulfate ion · ion · 2 copies · chains J, C, D, I, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 773 | 0.80 | 0.83 | 71 | empty |
| 2 | 965 | 0.74 | 0.77 | 62 | empty |
| 3 | 337 | 0.74 | 0.86 | 46 | empty |
| 4 | 451 | 0.73 | 0.83 | 56 | empty |
| 5 | 827 | 0.71 | 0.77 | 84 | empty |
Interfaces
37 interfaces between chains.
- I–J · 6443 Ų buried · 567 hydrogen bonds · nucleic-nucleic
- E–F · 2652 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 2628 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 2597 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2567 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
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 P06897
- Every structure of UniProt P02281
- Elsewhere: RCSB PDB 4WU8 · PDBe 4WU8 · UniProt P84233 · UniProt P62799 · UniProt P06897 · UniProt P02281
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