MolNFT v1 · #85003 · DNA
Intercalation and major groove recognition in the 1.2 a resolution crystal structure of RH[ME2TRIEN]PHI bound to 5'-G(5IU)TGCAAC-3'
454D · 5'-D(*GP*(5IU)P*TP*GP*CP*AP*AP*C)-3': “Intercalation and major groove recognition in the 1.2 a resolution crystal structure of RH[ME2TRIEN]PHI bound…”. X-ray diffraction, 1 ligand (RHM), 3 pockets (best druggability 0.58). MolNFT v1…
- PDB
- 454D
- Type
- DNA
- Length
- 80 nucleotides
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*(5IU)P*TP*GP*CP*AP*AP*C)-3'
- Ligands
- RHM
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | 5'-D(*GP*(5IU)P*TP*GP*CP*AP*AP*C)-3' | dna | 8 | — | — |
Ligands and binding sites
- RHM · Delta-alpha-rh[2r,9r-diamino-4,7-diazadecane]9,10-phenanthrenequinone diimine · ligand · 5 copies · chains A, B, C, D, E, F, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 449 | 0.58 | 0.75 | 18 | empty |
| 2 | 55 | 0.25 | 0.73 | 7 | empty |
| 3 | 54 | 0.23 | 0.72 | 7 | RHM |
Interfaces
20 interfaces between chains.
- E–F · 370 Ų buried · 26 hydrogen bonds · nucleic-nucleic
- G–H · 369 Ų buried · 30 hydrogen bonds · nucleic-nucleic
- A–B · 369 Ų buried · 26 hydrogen bonds · nucleic-nucleic
- I–J · 368 Ų buried · 32 hydrogen bonds · nucleic-nucleic
- C–D · 367 Ų buried · 32 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 10 modified (nucleotide modification).
Compared structures
- 454D · Intercalation and major groove recognition in the 1.2 a resolution crystal structure of… · 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 454D · PDBe 454D
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