Research workbench
Structural basis for reactivation of -146C>T mutant tert promoter by cooperative binding of P52 and ETS1/2
Analyse Structural basis for reactivation of -146C>T mutant tert promoter by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZMC
- Type
- protein + DNA
- Length
- 241 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(P*CP*GP*GP*GP*GP*AP*CP*CP*CP*GP*GP*AP*AP*GP*GP*G)-3'); DNA (5'…
- UniProt
- P14921, Q00653
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (5'- D(P*CP*GP*GP*GP*GP*AP*CP*CP*CP*GP*GP*AP*AP*GP*GP*G)-3') | dna | 16 | — | — |
| D | DNA (5'- D(P*GP*CP*CP*CP*TP*TP*CP*CP*GP*GP*GP*TP*CP*CP*CP*C)-3') | dna | 16 | — | — |
| B | Protein C-ets-1 | protein | 106 | 42% helix, 11% strand | P14921 |
| A | Nuclear factor nf-kappa-B P100 subunit | protein | 103 | 3% helix, 45% strand | Q00653 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 379 | 0.62 | 0.78 | 47 | empty |
| 2 | 124 | 0.46 | 0.78 | 18 | empty |
| 3 | 63 | 0.29 | 0.74 | 13 | empty |
| 4 | 63 | 0.27 | 0.73 | 15 | empty |
Interfaces
4 interfaces between chains.
- C–D · 677 Ų buried · 66 hydrogen bonds · nucleic-nucleic
- B–A · 671 Ų buried · 8 hydrogen bonds · protein-protein
- D–B · 478 Ų buried · 8 hydrogen bonds · protein-nucleic
- C–B · 421 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 5ZMC · Structural Basis for Reactivation of -146C>T Mutant TERT Promoter by cooperative binding… · the same entry in another collection · chain C against C, TM-score 1.00
- Q00653 · AlphaFold monomer V2.0 prediction for nuclear factor nf-kappa-B P100 subunit (Q00653) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P14921 · AlphaFold monomer V2.0 prediction for protein C-ets-1 (P14921) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P14921
- Every structure of UniProt Q00653
- Elsewhere: RCSB PDB 5ZMC · PDBe 5ZMC · UniProt P14921 · UniProt Q00653
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