Research workbench
Crystal structure of the brct domains of 53BP1 in complex with P53 and H2AX-PSER139 (GAMMAH2AX)
Analyse Crystal structure of the brct domains of 53BP1 in complex with P53 and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ECG
- Type
- protein
- Length
- 833 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellular tumor antigen P53; Tumor suppressor P53-binding protein 1; Sep-gln-glu-tyr
- UniProt
- P04637, Q12888
- Ligands
- ZN
- Pockets
- 16 · best druggability 0.46
Structure
x-ray diffraction · 5 distinct chains · 22% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cellular tumor antigen P53 | protein | 192 | 11% helix, 34% strand | P04637 |
| B | Cellular tumor antigen P53 | protein | 183 | 9% helix, 36% strand | P04637 |
| C | Tumor suppressor P53-binding protein 1 | protein | 227 | 33% helix, 19% strand | Q12888 |
| D | Tumor suppressor P53-binding protein 1 | protein | 223 | 33% helix, 17% strand | Q12888 |
| E, F | Sep-gln-glu-tyr | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.46 | 0.78 | 25 | empty |
| 2 | 124 | 0.46 | 0.78 | 22 | empty |
| 3 | 112 | 0.42 | 0.77 | 23 | empty |
| 4 | 127 | 0.41 | 0.75 | 18 | empty |
| 5 | 121 | 0.40 | 0.75 | 21 | empty |
Interfaces
6 interfaces between chains.
- A–C · 589 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 551 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 471 Ų buried · 6 hydrogen bonds · protein-protein
- C–F · 438 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 438 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 2 modified (disulfide, phosphorylation).
Compared structures
- 5ECG · Crystal structure of the BRCT domains of 53BP1 in complex with p53 and H2AX-pSer139… · the same entry in another collection · chain F against F, TM-score 1.00
- Q12888 · AlphaFold monomer V2.0 prediction for TP53-binding protein 1 (Q12888) · a predicted model of the same protein · chain D against A, TM-score 0.99
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
- Every structure of UniProt Q12888
- Elsewhere: RCSB PDB 5ECG · PDBe 5ECG · UniProt P04637 · UniProt Q12888
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