7DVD: P53 DNA binding domain and PUMA complex
The crystal structure of p53 DNA binding domain and PUMA complex. Determined by X-ray diffraction at 2.59 Å resolution. Released 4 Aug 2021.
- Method
- X-ray diffraction
- Resolution
- 2.59 Å
- Organism
- Homo sapiens
- Chains
- 5
- Atoms
- 6,412
- Mol. weight
- 94.85 kDa
- Ligands
- ZN
- Released
- 4 Aug 2021
Explore 7DVD in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7DVD contains 22 α-helices and 56 β-strands across 5 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 5 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 93 | 1 | 1 |
| β-strand | 103 | 1 | 2 |
| β-strand | 110-112 | 3 | 3 |
| β-strand | 124-127 | 4 | 2 |
| β-strand | 132-136 | 5 | 2 |
| β-strand | 141-146 | 6 | 3 |
| β-strand | 156-163 | 8 | 2 |
| α-helix | 166-168 | 3 | |
| β-strand | 171 | 1 | 1 |
| α-helix | 172-173 | 2 | |
| α-helix | 177-180 | 4 | |
| β-strand | 195-198 | 4 | 3 |
| β-strand | 204-207 | 4 | 2 |
| β-strand | 214-219 | 6 | 2 |
| α-helix | 222-224 | 3 | |
| β-strand | 225 | 1 | 4 |
| β-strand | 227 | 1 | 4 |
| β-strand | 230-236 | 7 | 3 |
| β-strand | 251-258 | 8 | 2 |
| β-strand | 264-275 | 12 | 2 |
| α-helix | 278-288 | 11 | |
Chain B: 5 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 103 | 1 | 5 |
| β-strand | 110-112 | 3 | 6 |
| β-strand | 124-127 | 4 | 5 |
| β-strand | 132-136 | 5 | 5 |
| β-strand | 141-146 | 6 | 6 |
| α-helix | 150-152 | 3 | |
| β-strand | 156-163 | 8 | 5 |
| α-helix | 166-168 | 3 | |
| α-helix | 172-173 | 2 | |
| α-helix | 177-180 | 4 | |
| β-strand | 195-197 | 3 | 6 |
| β-strand | 204-207 | 4 | 5 |
| β-strand | 214-219 | 6 | 5 |
| β-strand | 230-236 | 7 | 6 |
| β-strand | 251-258 | 8 | 5 |
| β-strand | 264-275 | 12 | 5 |
| α-helix | 278-288 | 11 | |
Chain C: 5 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 93 | 1 | 7 |
| β-strand | 103 | 1 | 8 |
| β-strand | 110-112 | 3 | 9 |
| β-strand | 116 | 1 | 2 |
| β-strand | 124-127 | 4 | 8 |
| β-strand | 132-135 | 4 | 8 |
| β-strand | 141-146 | 6 | 9 |
| α-helix | 150-152 | 3 | |
| β-strand | 156-163 | 8 | 8 |
| α-helix | 166-168 | 3 | |
| β-strand | 171 | 1 | 7 |
| α-helix | 177-180 | 4 | |
| β-strand | 195-198 | 4 | 9 |
| β-strand | 204-207 | 4 | 8 |
| β-strand | 214-219 | 6 | 8 |
| α-helix | 222-224 | 3 | |
| β-strand | 230-236 | 7 | 9 |
| β-strand | 251-258 | 8 | 8 |
| β-strand | 264-274 | 11 | 8 |
| α-helix | 278-288 | 11 | |
Chain D: 6 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 103 | 1 | 10 |
| β-strand | 110-112 | 3 | 11 |
| β-strand | 116 | 1 | 5 |
| β-strand | 124-127 | 4 | 10 |
| β-strand | 132-135 | 4 | 10 |
| β-strand | 141-146 | 6 | 11 |
| α-helix | 150-152 | 3 | |
| β-strand | 156-163 | 8 | 10 |
| α-helix | 166-168 | 3 | |
| α-helix | 172-173 | 2 | |
| α-helix | 177-181 | 5 | |
| β-strand | 195-197 | 3 | 11 |
| β-strand | 204-207 | 4 | 10 |
| β-strand | 214-219 | 6 | 10 |
| α-helix | 220-224 | 5 | |
| β-strand | 230-236 | 7 | 11 |
| β-strand | 251-258 | 8 | 10 |
| β-strand | 264-274 | 11 | 10 |
| α-helix | 278-287 | 10 | |
Chain E: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-11 | 3 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Cellular tumor antigen p53 | A, B, C, D | protein | 205 | Homo sapiens | P04637 (AlphaFold model) |
| Bcl-2-binding component 3, isoforms 1/2 | E | protein | 15 | Homo sapiens | Q9BXH1 (AlphaFold model) |
Sequence of entity 1 (A, B, C, D), FASTA
>7DVD_1 Cellular tumor antigen p53 (chains A, B, C, D)
PLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTP
PPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNT
FRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFE
VRVCACPGRDRRTEEENLRHHHHHH
Sequence of entity 2 (E), FASTA
>7DVD_2 Bcl-2-binding component 3, isoforms 1/2 (chains E)
EIGAQLRRMADDLNA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 4 |
Primary citation
Structural basis of the p53 DNA binding domain and PUMA complex. Han, C.W., Lee, H.N., Jeong, M.S. et al. Biochem Biophys Res Commun (2021) 548:39-46. DOI 10.1016/j.bbrc.2021.02.049 · PubMed
Other PDB entries of the same protein (UniProt P04637 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9C5S 1.01 Å, Disulfide-linked, antiparallel p53-derived peptide dimer (CV1)
- 3D06 1.2 Å, Human p53 core domain with hot spot mutation R249S (I)
- 5MHC 1.2 Å, Crystal structure of 14-3-3sigma and a p53 C-terminal 12-mer synthetic phosphopeptide
- 8UQR 1.22 Å, Crystal structure of the human p53 tetramerization domain
- 6GGC 1.24 Å, p53 cancer mutant Y220C in complex with small-molecule stabilizer PK9320
- 6SHZ 1.24 Å, p53 cancer mutant Y220C
- 4MZI 1.25 Å, Crystal structure of a human mutant p53
- 6GGE 1.25 Å, p53 cancer mutant Y220C in complex with small-molecule stabilizer PK9327
- 3LW1 1.28 Å, Binary complex of 14-3-3 sigma and p53 pT387-peptide
- 5O1E 1.3 Å, p53 cancer mutant Y220C im complex with compound MB577
- 6RL3 1.3 Å, Fragment AZ-003 binding at the p53pT387/14-3-3 sigma interface
- 8E7A 1.3 Å, Crystal structure of the p53 (Y107H) core domain orthorhombic P form
Browse structure collections
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