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Structural basis of G-quadruplex DNA recognition by the yeast telomeric protein Rap1
Analyse Structural basis of G-quadruplex DNA recognition by the yeast telomeric protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LDM
- Type
- protein + DNA
- Length
- 209 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c); SYNTHETIC CONSTRUCT
- Molecule
- DNA-binding protein RAP1; G-guadruplex DNA
- UniProt
- P11938
- Ligands
- NA, K
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · resolution 2.4 · 2 distinct chains · 49% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-binding protein RAP1 | protein | 191 | 49% helix, 5% strand | P11938 |
| B | G-guadruplex DNA | dna | 18 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 11 copies · chains A, B
- K · Potassium ion · metal · 5 copies · chains B
- GOL · Glycerol · additive · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 370 | 0.66 | 0.80 | 32 | NA |
| 2 | 83 | 0.43 | 0.80 | 15 | TRS |
Interfaces
1 interface between chains.
- A–B · 639 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 6LDM · Structural basis of G-quadruplex DNA recognition by the yeast telomeric protein RAP1 · the same entry in another collection · chain A against A, TM-score 1.00
- P11938 · AlphaFold monomer V2.0 prediction for DNA-binding protein RAP1 (P11938) · a predicted model of the same protein · chain A against A, TM-score 0.60
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 P11938
- Elsewhere: RCSB PDB 6LDM · PDBe 6LDM · UniProt P11938
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