SMTL ID : 6ldm.1

Structural basis of G-quadruplex DNA recognition by the yeast telomeric protein Rap1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 2 residues within 4Å: Chain A: F.242, M.267 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.267

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 7 residues within 4Å: Chain A: T.78, H.79, T.80, K.140, R.141, T.231, A.234 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:H.79, A:H.79, A:T.80, A:T.80, A:K.140, A:K.140, A:R.141, A:T.231 Water bridges: A:T.80

11 x NA: SODIUM ION(Non-functional Binders)

NA.3: 6 residues within 4Å: Chain A: H.99, R.102, V.103 Chain B: G.13, T.18 Ligands: NA.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.102 NA.4: 3 residues within 4Å: Chain A: N.95, R.98, H.99 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.95, A:N.95, A:R.98 NA.5: 4 residues within 4Å: Chain A: A.55, F.57 Chain B: G.12, G.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.55 NA.11: 5 residues within 4Å: Chain B: G.8, G.9, T.10, G.11, G.12 No protein-ligand interaction detected (PLIP) NA.12: 2 residues within 4Å: Chain B: G.3, G.4 No protein-ligand interaction detected (PLIP) NA.13: 5 residues within 4Å: Chain B: G.4, G.5, T.6, G.7 Ligands: NA.15 No protein-ligand interaction detected (PLIP) NA.14: 8 residues within 4Å: Chain A: V.103 Chain B: G.5, G.9, G.13, G.17, T.18 Ligands: NA.3, K.6 No protein-ligand interaction detected (PLIP) NA.15: 4 residues within 4Å: Chain B: T.6, G.7, G.8 Ligands: NA.13 No protein-ligand interaction detected (PLIP) NA.16: 3 residues within 4Å: Chain B: G.7, G.8, G.11 No protein-ligand interaction detected (PLIP) NA.17: 3 residues within 4Å: Chain B: G.3, G.15, G.16 No protein-ligand interaction detected (PLIP) NA.18: 2 residues within 4Å: Chain B: G.13, G.16 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.99

5 x K: POTASSIUM ION(Non-functional Binders)

K.6: 10 residues within 4Å: Chain B: G.4, G.5, G.8, G.9, G.12, G.13, G.16, G.17 Ligands: K.7, NA.14 No protein-ligand interaction detected (PLIP) K.7: 10 residues within 4Å: Chain B: G.3, G.4, G.7, G.8, G.11, G.12, G.15, G.16 Ligands: K.6, K.8 No protein-ligand interaction detected (PLIP) K.8: 5 residues within 4Å: Chain B: G.3, G.7, G.11, G.15 Ligands: K.7 No protein-ligand interaction detected (PLIP) K.9: 1 residues within 4Å: Chain B: G.3 No protein-ligand interaction detected (PLIP) K.10: 1 residues within 4Å: Chain B: T.18 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Traczyk, A. et al., Structural basis of G-quadruplex DNA recognition by the yeast telomeric protein Rap1. Nucleic Acids Res. (2020)

Release Date

2020-03-18

Peptides

DNA-binding protein RAP1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA-binding protein RAP1