MolNFT v1 · #69303 · protein + DNA
Crystal structure of the P53 core domain bound to a full consensus site as a self-assembled tetramer
3KMD · Cellular tumor antigen P53: “Crystal structure of the P53 core domain bound to a full consensus site as a self-assembled tetramer”. X-ray diffraction, 1 ligand (ZN), 14 pockets (best druggability 0.71). MolNFT v1 #69303 on…
- PDB
- 3KMD
- Type
- protein + DNA
- Length
- 838 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellular tumor antigen P53; 5'-D(*GP*GP*GP*CP*AP*TP*GP*CP*CP*TP*AP*GP*GP*CP*AP*TP*GP*CP…
- UniProt
- P04637
- Ligands
- ZN
- Pockets
- 14 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, C | Cellular tumor antigen P53 | protein | 200 | 11% helix, 34% strand | P04637 |
| E, F | 5'-D(*GP*GP*GP*CP*AP*TP*GP*CP*CP*TP*AP*GP*GP*CP*AP*TP*GP*CP *C)-3' | dna | 19 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 596 | 0.71 | 0.80 | 59 | empty |
| 2 | 437 | 0.69 | 0.81 | 53 | empty |
| 3 | 344 | 0.66 | 0.80 | 35 | empty |
| 4 | 298 | 0.64 | 0.81 | 33 | empty |
| 5 | 172 | 0.44 | 0.75 | 27 | empty |
Interfaces
13 interfaces between chains.
- E–F · 881 Ų buried · 90 hydrogen bonds · nucleic-nucleic
- A–D · 464 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 422 Ų buried · 4 hydrogen bonds · protein-protein
- D–C · 405 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 399 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3KMD · Crystal structure of the p53 core domain bound to a full consensus site as a… · 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 3KMD · PDBe 3KMD · UniProt P04637
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