Research workbench
P53 core domain in complex with DNA
Analyse P53 core domain in complex with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TSR
- Type
- protein + DNA
- Length
- 627 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*TP*TP*TP*CP*CP*TP*AP*GP*AP*CP*TP*TP*GP*CP*CP*CP*A P*AP*TP*TP*A)-3'); DNA (5'…
- UniProt
- P04637
- Ligands
- ZN
- Pockets
- 8 · best druggability 0.66
Structure
x-ray diffraction · 5 distinct chains · 9% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | DNA (5'- D(*TP*TP*TP*CP*CP*TP*AP*GP*AP*CP*TP*TP*GP*CP*CP*CP*A P*AP*TP*TP*A)-3') | dna | 21 | — | — |
| F | DNA (5'- D(*AP*TP*AP*AP*TP*TP*GP*GP*GP*CP*AP*AP*GP*TP*CP*TP*A P*GP*GP*AP*A)-3') | dna | 21 | — | — |
| A | Protein (P53 tumor suppressor) | protein | 196 | 9% helix, 34% strand | P04637 |
| B | Protein (P53 tumor suppressor) | protein | 194 | 10% helix, 34% strand | P04637 |
| C | Protein (P53 tumor suppressor) | protein | 195 | 10% helix, 34% strand | P04637 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 522 | 0.66 | 0.78 | 32 | empty |
| 2 | 405 | 0.62 | 0.77 | 36 | empty |
| 3 | 491 | 0.59 | 0.74 | 64 | empty |
| 4 | 323 | 0.58 | 0.76 | 34 | empty |
| 5 | 155 | 0.46 | 0.76 | 19 | empty |
Interfaces
9 interfaces between chains.
- E–F · 884 Ų buried · 103 hydrogen bonds · nucleic-nucleic
- A–B · 757 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 400 Ų buried · 3 hydrogen bonds · protein-protein
- E–B · 349 Ų buried · 8 hydrogen bonds · protein-nucleic
- F–B · 324 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 1TSR · P53 core domain in complex with DNA · the same entry in another collection · chain E against E, 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 P04637
- Elsewhere: RCSB PDB 1TSR · PDBe 1TSR · UniProt P04637
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