Research workbench
Radiation damage to the nucleoprotein complex C.ESP1396I: dose (dwd) 2.1 mgy
Analyse Radiation damage to the nucleoprotein complex C.ESP1396I: dose (dwd) 2.1 mgy in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X4B
- 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
- Ligands
- MG
- Pockets
- 8 · best druggability 0.51
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 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains D, E, A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 213 | 0.51 | 0.77 | 22 | empty |
| 2 | 155 | 0.44 | 0.76 | 19 | empty |
| 3 | 65 | 0.37 | 0.79 | 13 | empty |
| 4 | 99 | 0.35 | 0.74 | 15 | empty |
| 5 | 69 | 0.33 | 0.77 | 14 | empty |
Interfaces
12 interfaces between chains.
- E–F · 1589 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 · 442 Ų buried · 8 hydrogen bonds · protein-nucleic
- C–E · 428 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 4X4B · RADIATION DAMAGE TO THE NUCLEOPROTEIN COMPLEX C.Esp1396I: DOSE (DWD) 2.1 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 4X4B · PDBe 4X4B · UniProt Q8GGH0
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