3QYM: P63 DNA Binding Domain
Structure of p63 DNA Binding Domain in Complex with a 10 Base Pair A/T Rich Response Element Half Site. Determined by X-ray diffraction at 3.2 Å resolution. Released 6 Apr 2011.
- Method
- X-ray diffraction
- Resolution
- 3.2 Å
- Organism
- Homo sapiens
- Chains
- 16
- Atoms
- 13,681
- Mol. weight
- 206.34 kDa
- Ligands
- ZN
- Released
- 6 Apr 2011
Explore 3QYM in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
3QYM contains 19 α-helices and 121 β-strands across 8 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: 3 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 132 | 1 | 1 |
| β-strand | 139-141 | 3 | 2 |
| β-strand | 153-156 | 4 | 1 |
| β-strand | 161-164 | 4 | 1 |
| β-strand | 173-175 | 3 | 2 |
| β-strand | 185-192 | 8 | 1 |
| α-helix | 195-198 | 4 | |
| β-strand | 226-228 | 3 | 3 |
| β-strand | 235-238 | 4 | 1 |
| β-strand | 245-248 | 4 | 1 |
| β-strand | 250 | 1 | 1 |
| α-helix | 253-255 | 3 | |
| β-strand | 256 | 1 | 4 |
| β-strand | 258 | 1 | 4 |
| β-strand | 265-267 | 3 | 3 |
| β-strand | 282-289 | 8 | 1 |
| β-strand | 295-304 | 10 | 1 |
| α-helix | 311-319 | 9 | |
Chains B, F, G and H: 2 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 132 | 1 | 5 |
| β-strand | 139-141 | 3 | 6 |
| β-strand | 153-156 | 4 | 5 |
| β-strand | 161-164 | 4 | 5 |
| β-strand | 173-175 | 3 | 6 |
| β-strand | 185-192 | 8 | 5 |
| α-helix | 195-198 | 4 | |
| β-strand | 226-228 | 3 | 7 |
| β-strand | 235-238 | 4 | 5 |
| β-strand | 245-248 | 4 | 5 |
| β-strand | 250 | 1 | 5 |
| β-strand | 256 | 1 | 8 |
| β-strand | 258 | 1 | 8 |
| β-strand | 265-267 | 3 | 7 |
| β-strand | 282-289 | 8 | 5 |
| β-strand | 295-304 | 10 | 5 |
| α-helix | 311-319 | 9 | |
Chain C: 2 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 132 | 1 | 9 |
| β-strand | 139-141 | 3 | 10 |
| β-strand | 153-156 | 4 | 9 |
| β-strand | 161-164 | 4 | 9 |
| β-strand | 173-175 | 3 | 10 |
| β-strand | 185-192 | 8 | 9 |
| α-helix | 195-198 | 4 | |
| β-strand | 226-228 | 3 | 11 |
| β-strand | 235-238 | 4 | 9 |
| β-strand | 245-248 | 4 | 9 |
| β-strand | 250 | 1 | 9 |
| β-strand | 256 | 1 | 12 |
| β-strand | 258 | 1 | 12 |
| β-strand | 265-267 | 3 | 11 |
| β-strand | 282-289 | 8 | 9 |
| β-strand | 295-298 | 4 | 9 |
| β-strand | 301-304 | 4 | 9 |
| α-helix | 311-319 | 9 | |
Chain D: 3 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 126-128 | 3 | |
| β-strand | 132 | 1 | 13 |
| β-strand | 139-141 | 3 | 14 |
| β-strand | 153-156 | 4 | 13 |
| β-strand | 161-164 | 4 | 13 |
| β-strand | 173-175 | 3 | 14 |
| β-strand | 185-192 | 8 | 13 |
| α-helix | 195-198 | 4 | |
| β-strand | 226-228 | 3 | 15 |
| β-strand | 235-238 | 4 | 13 |
| β-strand | 245-248 | 4 | 13 |
| β-strand | 250 | 1 | 13 |
| β-strand | 256 | 1 | 16 |
| β-strand | 258 | 1 | 16 |
| β-strand | 265-267 | 3 | 15 |
| β-strand | 282-289 | 8 | 13 |
| β-strand | 295-304 | 10 | 13 |
| α-helix | 311-319 | 9 | |
Chain E: 3 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 126-128 | 3 | |
| β-strand | 132 | 1 | 17 |
| β-strand | 139-141 | 3 | 18 |
| β-strand | 153-156 | 4 | 17 |
| β-strand | 161-164 | 4 | 17 |
| β-strand | 173-175 | 3 | 18 |
| β-strand | 185-192 | 8 | 17 |
| α-helix | 195-198 | 4 | |
| β-strand | 226-228 | 3 | 19 |
| β-strand | 235-238 | 4 | 17 |
| β-strand | 245-248 | 4 | 17 |
| β-strand | 250 | 1 | 17 |
| β-strand | 256 | 1 | 20 |
| β-strand | 258 | 1 | 20 |
| β-strand | 265-267 | 3 | 19 |
| β-strand | 282-289 | 8 | 17 |
| β-strand | 295-304 | 10 | 17 |
| α-helix | 311-320 | 10 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Tumor protein 63 | A, B, C, D, E, F, G, H | protein | 203 | Homo sapiens | Q9H3D4 (AlphaFold model) |
| 5'-d(*ap*ap*ap*cp*ap*tp*gp*tp*tp*t)-3' | I, J, K, L, M, N, O, P | DNA | 10 | | |
Sequence of entity 1 (A, B, C, D, E, F, G, H), FASTA
>3QYM_1 Tumor protein 63 (chains A, B, C, D, E, F, G, H)
GSHMASPSNTDYPGPHSFDVSFQQSSTAKSATWTYSTELKKLYCQIAKTCPIQIKVMTPP
PQGAVIRAMPVYKKAEHVTEVVKRCPNHELSREFNEGQIAPPSHLIRVEGNSHAQYVEDP
ITGRQSVLVPYEPPQVGTEFTTVLYNFMCNSSCVGGMNRRPILIIVTLETRDGQVLGRRC
FEARICACPGRDRKADEDSIRKQ
Sequence of entity 2 (I, J, K, L, M, N, O, P), FASTA
>3QYM_2 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3' (chains I, J, K, L, M, N, O, P)
AAACATGTTT
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 8 |
Primary citation
Structures of p63 DNA binding domain in complexes with half-site and with spacer-containing full response elements. Chen, C., Gorlatova, N., Kelman, Z. et al. Proc Natl Acad Sci U S A (2011) 108:6456-6461. DOI 10.1073/pnas.1013657108 · PubMed
Other PDB entries of the same protein (UniProt Q9H3D4 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 2Y9U 1.6 Å, Structural basis of p63a SAM domain mutants involved in AEC syndrome
- 8P9C 1.76 Å, Crystal structure of p63-p73 heterotetramer (tetramerisation domain) in complex with…
- 7Z72 1.8 Å, Crystal structure of p63 SAM in complex with darpin A5
- 7Z7E 1.8 Å, Crystal structure of p63 DNA binding domain in complex with inhibitory DARPin G4
- 7Z71 1.85 Å, Crystal structure of p63 DBD in complex with darpin C14
- 3ZY0 1.9 Å, Crystal structure of a truncated variant of the human p63 tetramerization domain lacking…
- 6RU8 1.92 Å, Crystal structure of Casein Kinase I delta (CK1d) in complex with triple phosphorylated…
- 6RU6 2.05 Å, Crystal structure of Casein Kinase I delta (CK1d) in complex with monophosphorylated p63…
- 6RU7 2.08 Å, Crystal structure of Casein Kinase I delta (CK1d) in complex with double phosphorylated…
- 3ZY1 2.15 Å, Crystal structure of the human p63 tetramerization domain
- 9N54 2.2 Å, Bipartite p63 NLS in complex with Importin Alpha 2
- 8P9E 2.25 Å, Crystal structure of wild type p63-p73 heterotetramer (tetramerisation domain) in…
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