Research workbench
Crystal structure of the helical domain of S. pombe TBF1
Analyse Crystal structure of the helical domain of S. pombe TBF1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K5S
- Type
- protein
- Length
- 870 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Telomeric DNA-binding factor TRF1
- UniProt
- Q6E434
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Telomeric DNA-binding factor TRF1 | protein | 220 | 73% helix, 0% strand | Q6E434 |
| B | Telomeric DNA-binding factor TRF1 | protein | 216 | 71% helix, 0% strand | Q6E434 |
| C | Telomeric DNA-binding factor TRF1 | protein | 219 | 69% helix, 0% strand | Q6E434 |
| D | Telomeric DNA-binding factor TRF1 | protein | 215 | 72% helix, 0% strand | Q6E434 |
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1027 | 0.73 | 0.76 | 74 | empty |
| 2 | 584 | 0.67 | 0.77 | 67 | empty |
| 3 | 442 | 0.63 | 0.77 | 55 | empty |
| 4 | 394 | 0.57 | 0.75 | 52 | empty |
| 5 | 294 | 0.56 | 0.76 | 32 | empty |
Interfaces
5 interfaces between chains.
- B–D · 765 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 391 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 386 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 383 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 163 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6K5S · Crystal structure of the Helical domain of S. pombe Tbf1 · the same entry in another collection · chain D against D, TM-score 1.00
- Q6E434 · AlphaFold monomer V2.0 prediction for telomeric DNA-binding factor TRF1 (Q6E434) · 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 Q6E434
- Elsewhere: RCSB PDB 6K5S · PDBe 6K5S · UniProt Q6E434
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