Research workbench
ICP4 DNA-binding domain, lacking intrinsically disordered region, in complex with 12MER DNA duplex from its own promoter
Analyse ICP4 DNA-binding domain, lacking intrinsically disordered region, in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MHJ
- Type
- protein + DNA
- Length
- 399 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major viral transcription factor ICP4; DNA (5'-D(P*CP*GP*AP*TP*CP*GP*TP*CP*C)-3')
- UniProt
- P08392
- Ligands
- CL
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major viral transcription factor ICP4 | protein | 194 | 52% helix, 3% strand | P08392 |
| B | Major viral transcription factor ICP4 | protein | 187 | 56% helix, 3% strand | P08392 |
| E | DNA (5'-D(P*CP*GP*AP*TP*CP*GP*TP*CP*C)-3') | dna | 9 | — | — |
| F | DNA (5'-D(P*CP*GP*AP*TP*CP*GP*TP*CP*C)-3') | dna | 9 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 479 | 0.73 | 0.82 | 58 | empty |
| 2 | 526 | 0.67 | 0.78 | 48 | empty |
| 3 | 195 | 0.66 | 0.85 | 28 | empty |
| 4 | 105 | 0.45 | 0.79 | 17 | empty |
| 5 | 61 | 0.42 | 0.82 | 15 | ACY |
Interfaces
6 interfaces between chains.
- A–B · 2945 Ų buried · 34 hydrogen bonds · protein-protein
- E–F · 414 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- A–E · 345 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–E · 278 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–F · 218 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
- 5MHJ · ICP4 DNA-binding domain, lacking intrinsically disordered region, in complex with 12mer… · 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 P08392
- Elsewhere: RCSB PDB 5MHJ · PDBe 5MHJ · UniProt P08392
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