MolNFT v2 · #156657 · protein + DNA
Structural basis of G-quadruplex DNA recognition by the yeast telomeric protein Rap1
6LDM: “Structural basis of G-quadruplex DNA recognition by the yeast telomeric protein Rap1”. X-ray diffraction at 2.4, 2 ligands (NA, K). MolNFT v2 #156657 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- 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
- UniProt
- P11938
- Ligands
- NA, K
Structure
x-ray diffraction · resolution 2.4 · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | — | protein | 191 | — | P11938 |
| B | — | 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.
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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