Research workbench
Crystal structure of a polypeptide P53 mutant bound to DNA
Analyse Crystal structure of a polypeptide P53 mutant bound to DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MZR
- Type
- protein + DNA
- Length
- 988 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellular tumor antigen P53; Consensus DNA sense strand; Consensus DNA anti-sense strand
- UniProt
- P04637
- Ligands
- ZN
- Pockets
- 17 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cellular tumor antigen P53 | protein | 234 | 20% helix, 31% strand | P04637 |
| K | Consensus DNA sense strand | dna | 26 | — | — |
| L | Consensus DNA anti-sense strand | dna | 26 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1029 | 0.75 | 0.78 | 113 | empty |
| 2 | 613 | 0.70 | 0.78 | 73 | empty |
| 3 | 474 | 0.70 | 0.80 | 54 | empty |
| 4 | 462 | 0.69 | 0.80 | 37 | empty |
| 5 | 490 | 0.59 | 0.75 | 50 | empty |
Interfaces
13 interfaces between chains.
- A–C · 2013 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 1914 Ų buried · 30 hydrogen bonds · protein-protein
- K–L · 1112 Ų buried · 106 hydrogen bonds · nucleic-nucleic
- B–L · 400 Ų buried · 9 hydrogen bonds · protein-nucleic
- C–D · 398 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4MZR · Crystal structure of a polypeptide p53 mutant bound to DNA · the same entry in another collection · chain B against B, 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 4MZR · PDBe 4MZR · UniProt P04637
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.