SMTL ID : 9dou.1

Taeniopygia guttata R2 retrotransposon (R2Tg) initiating target-primed reverse transcription

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.777, I.778, D.878, K.912 Ligands: TTP.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.777, A:I.778, A:D.878

1 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.2: 16 residues within 4Å: Chain A: K.697, R.711, D.777, I.778, A.779, K.780, A.781, F.782, Q.837, D.878, Q.909, K.912 Chain C: T.13 Chain D: A.324, A.325 Ligands: MG.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.782 Hydrogen bonds: A:K.780, A:A.781, A:F.782, A:Q.909 Salt bridges: A:K.697, A:K.697, A:R.711, A:R.711, A:K.912, A:K.912

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.297, C.300, H.313, H.318 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.297, A:C.300, A:H.313, A:H.318 ZN.4: 4 residues within 4Å: Chain A: C.1212, C.1215, H.1224, C.1229 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.1212, A:C.1215, A:H.1224, A:C.1229 ZN.5: 4 residues within 4Å: Chain A: C.262, C.265, H.278, C.282 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.262, A:C.265, A:H.278, A:C.282 ZN.6: 5 residues within 4Å: Chain A: C.232, C.234, C.235, H.248, H.253 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.232, A:H.248, A:H.253

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Edmonds, K.H.K. et al., Structure and biochemistry-guided engineering of an all-RNA system for DNA insertion with R2 retrotransposons. To Be Published

Release Date

2025-05-21

Peptides

R2Tg retrotransposon ORF: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

R2Tg retrotransposon ORF