MolNFT v1 · #94951 · protein + DNA
Human P53 core domain with hot spot mutation R273C and second-site suppressor mutation T284R in sequence-specific complex with DNA
4IBU · Cellular tumor antigen P53: “Human P53 core domain with hot spot mutation R273C and second-site suppressor mutation T284R in…”. X-ray diffraction, 1 ligand (ZN), 15 pockets (best druggability 0.75). MolNFT v1 #94951 on GenesisL1: 3D…
- PDB
- 4IBU
- Type
- protein + DNA
- Length
- 832 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellular tumor antigen P53; DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3')
- UniProt
- P04637
- Ligands
- ZN
- Pockets
- 15 · best druggability 0.75
Structure
x-ray diffraction · 7 distinct chains · 8% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cellular tumor antigen P53 | protein | 197 | 8% helix, 34% strand | P04637 |
| B | Cellular tumor antigen P53 | protein | 198 | 8% helix, 33% strand | P04637 |
| C | Cellular tumor antigen P53 | protein | 195 | 9% helix, 34% strand | P04637 |
| D | Cellular tumor antigen P53 | protein | 196 | 9% helix, 33% strand | P04637 |
| E | DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3') | dna | 11 | — | — |
| F | DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3') | dna | 11 | — | — |
| G, H | DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3') | dna | 12 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 16 copies · chains A, E, B, C, D
- ACT · Acetate ion · additive · 2 copies · chains B, C, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 837 | 0.75 | 0.79 | 65 | empty |
| 2 | 661 | 0.75 | 0.81 | 57 | empty |
| 3 | 160 | 0.50 | 0.79 | 23 | empty |
| 4 | 111 | 0.45 | 0.79 | 19 | EDO |
| 5 | 108 | 0.40 | 0.76 | 20 | empty |
Interfaces
19 interfaces between chains.
- G–H · 578 Ų buried · 57 hydrogen bonds · nucleic-nucleic
- E–F · 530 Ų buried · 54 hydrogen bonds · nucleic-nucleic
- C–G · 361 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–F · 350 Ų buried · 5 hydrogen bonds · protein-nucleic
- B–E · 348 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 4IBU · Human p53 core domain with hot spot mutation R273C and second-site suppressor mutation… · 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 P04637
- Elsewhere: RCSB PDB 4IBU · PDBe 4IBU · UniProt P04637
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.