Research workbench
Human P53 core domain with hot spot mutation R273C and second-site suppressor mutation T284R
Analyse Human P53 core domain with hot spot mutation R273C and second-site suppressor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IBZ
- Type
- protein
- Length
- 769 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellular tumor antigen P53
- UniProt
- P04637
- Ligands
- ZN
- Pockets
- 10 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cellular tumor antigen P53 | protein | 193 | 8% helix, 34% strand | P04637 |
| B | Cellular tumor antigen P53 | protein | 192 | 7% helix, 34% strand | P04637 |
| C | Cellular tumor antigen P53 | protein | 192 | 8% helix, 34% strand | P04637 |
| D | Cellular tumor antigen P53 | protein | 192 | 9% helix, 34% strand | P04637 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 19 copies · chains A, B, D, C
- ACT · Acetate ion · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 606 | 0.65 | 0.76 | 77 | EDO |
| 2 | 529 | 0.62 | 0.75 | 71 | EDO |
| 3 | 262 | 0.50 | 0.74 | 28 | EDO, ACT |
| 4 | 59 | 0.44 | 0.83 | 15 | empty |
| 5 | 104 | 0.39 | 0.76 | 17 | EDO |
Interfaces
4 interfaces between chains.
- A–C · 553 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 480 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 460 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 173 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4IBZ · 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 4IBZ · PDBe 4IBZ · UniProt P04637
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