MolNFT v1 · #109495 · protein + DNA
Radiation damage to the nucleoprotein complex C.ESP1396I: dose (dwd) 20.6 mgy
4X4F · Regulatory protein: “Radiation damage to the nucleoprotein complex C.ESP1396I: dose (dwd) 20.6 mgy”. X-ray diffraction, 8 pockets (best druggability 0.52). MolNFT v1 #109495 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4X4F
- Type
- protein + DNA
- Length
- 376 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Regulatory protein; 35-mer DNA
- UniProt
- Q8GGH0
- Pockets
- 8 · best druggability 0.52
Structure
x-ray diffraction · 4 distinct chains · 72% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Regulatory protein | protein | 76 | 72% helix, 1% strand | Q8GGH0 |
| B, C | Regulatory protein | protein | 77 | 71% helix, 1% strand | Q8GGH0 |
| E | 35-mer DNA | dna | 35 | — | — |
| F | 35-mer DNA | dna | 35 | — | — |
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.52 | 0.76 | 23 | empty |
| 2 | 157 | 0.44 | 0.76 | 19 | empty |
| 3 | 67 | 0.38 | 0.79 | 13 | empty |
| 4 | 106 | 0.36 | 0.74 | 16 | empty |
| 5 | 68 | 0.33 | 0.77 | 15 | empty |
Interfaces
12 interfaces between chains.
- E–F · 1588 Ų buried · 124 hydrogen bonds · nucleic-nucleic
- A–B · 1000 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 989 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 443 Ų buried · 8 hydrogen bonds · protein-nucleic
- C–E · 429 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 4X4F · RADIATION DAMAGE TO THE NUCLEOPROTEIN COMPLEX C.Esp1396I: DOSE (DWD) 20.6 MGy · 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 Q8GGH0
- Elsewhere: RCSB PDB 4X4F · PDBe 4X4F · UniProt Q8GGH0
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