Research workbench
Crystal structure of hydrogen peroxide treated zebrafish TRF2 complexed with DNA
Analyse Crystal structure of hydrogen peroxide treated zebrafish TRF2 complexed with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7C4R
- Type
- protein + DNA
- Length
- 154 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Terfa protein; DNA (5'- D(*D*TP*DP*TP*DP*AP*DP*GP*DP*GP*DP*GP*DP*TP*DP*TP*DP*AP*DP*GP*DP*G…
- UniProt
- Q4QRH9
- Pockets
- 3 · best druggability 0.49
Structure
x-ray diffraction · 4 distinct chains · 63% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Terfa protein | protein | 54 | 63% helix, 0% strand | Q4QRH9 |
| C | DNA (5'- D(*D*TP*DP*TP*DP*AP*DP*GP*DP*GP*DP*GP*DP*TP*DP*TP*DP*AP*DP*GP*DP*GP*D P*G)-3') | dna | 12 | — | — |
| D, F | DNA (5'- D(*D*CP*DP*CP*DP*CP*DP*TP*DP*AP*DP*AP*DP*CP*DP*CP*DP*CP*DP*TP*DP*AP*D P*A)-3') | dna | 12 | — | — |
| E | DNA (5'- D(*D*TP*DP*TP*DP*AP*DP*GP*DP*GP*DP*GP*DP*TP*DP*TP*DP*AP*DP*G)-3') | dna | 10 | — | — |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 231 | 0.49 | 0.75 | 27 | empty |
| 2 | 85 | 0.41 | 0.79 | 15 | empty |
| 3 | 50 | 0.31 | 0.77 | 8 | empty |
Interfaces
8 interfaces between chains.
- C–D · 544 Ų buried · 59 hydrogen bonds · nucleic-nucleic
- B–F · 462 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–D · 460 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–C · 456 Ų buried · 9 hydrogen bonds · protein-nucleic
- E–F · 452 Ų buried · 39 hydrogen bonds · nucleic-nucleic
Compared structures
- 7C4R · Crystal structure of hydrogen peroxide treated zebrafish TRF2 complexed with DNA · 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 Q4QRH9
- Elsewhere: RCSB PDB 7C4R · PDBe 7C4R · UniProt Q4QRH9
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