Research workbench
Structural studies of transcription factor P73 DNA binding domain bound to PA26 20-mer response element
Analyse Structural studies of transcription factor P73 DNA binding domain bound to PA26… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KBD
- Type
- protein + DNA
- Length
- 422 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor protein P73; DNA (5'-D(P*GP*GP*AP*CP*AP*AP*GP*TP*CP*T)-3'); DNA…
- UniProt
- O15350
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tumor protein P73 | protein | 201 | 9% helix, 32% strand | O15350 |
| C | DNA (5'-D(P*GP*GP*AP*CP*AP*AP*GP*TP*CP*T)-3') | dna | 10 | — | — |
| D | DNA (5'-D(P*AP*GP*AP*CP*TP*TP*GP*TP*CP*C)-3') | dna | 10 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 437 | 0.70 | 0.81 | 52 | empty |
| 2 | 250 | 0.50 | 0.75 | 31 | empty |
| 3 | 171 | 0.44 | 0.75 | 25 | empty |
| 4 | 100 | 0.44 | 0.79 | 18 | empty |
| 5 | 105 | 0.43 | 0.78 | 19 | empty |
Interfaces
6 interfaces between chains.
- C–D · 450 Ų buried · 31 hydrogen bonds · nucleic-nucleic
- B–D · 358 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–C · 345 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–B · 272 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 196 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 5KBD · Structural Studies of Transcription Factor p73 DNA Binding Domain Bound to PA26 20-mer… · 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 O15350
- Elsewhere: RCSB PDB 5KBD · PDBe 5KBD · UniProt O15350
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