SMTL ID : 8c8j.1

Long Interspersed Nuclear Element 1 (LINE-1) reverse transcriptase ternary complex with hybrid duplex and dTTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x DG- DC- DG- DC- DT- DT- DT- DC- DC: DNA (5'-D(P*GP*CP*GP*CP*TP*TP*TP*CP*C)-3')(Non-covalent)

DG-DC-DG-DC-DT-DT-DT-DC-DC.1: 20 residues within 4Å: Chain A: F.329, F.463, D.465, D.466, L.532, G.533, M.578, P.582, K.583, Y.586 Chain B: G.4, G.5, A.6, A.7, A.8, G.9, C.10, G.11, C.12 Ligands: TTP.3 Protein-ligand interaction information (PLIP) not available

2 x CIT: CITRIC ACID(Non-functional Binders)

CIT.2: 7 residues within 4Å: Chain A: K.319, K.320, I.322, H.323, H.324, R.440 Ligands: MG.21 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.324 Water bridges: A:H.324 Salt bridges: A:K.319, A:K.319, A:H.323, A:H.324, A:R.440 CIT.14: 8 residues within 4Å: Chain A: Q.502, A.525, S.526, K.527, R.528, I.529, K.530, Q.535 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:R.528 Hydrogen bonds: A:Q.502, A:S.526, A:K.527, A:R.528, A:K.530 Salt bridges: A:K.527, A:K.527, A:R.528

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

TTP.3: 16 residues within 4Å: Chain A: K.282, R.294, D.363, A.364, E.365, K.366, A.367, F.368, Q.422, D.465, N.497, K.500 Chain B: A.3, G.4 Ligands: DG-DC-DG-DC-DT-DT-DT-DC-DC.1, MG.22 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:F.368, A:Q.422 Hydrogen bonds: A:R.294, A:K.366, A:A.367, A:F.368, A:Q.422, A:N.497 Water bridges: A:K.282, A:K.282, A:R.294, A:R.294, A:K.500, A:K.500 Salt bridges: A:K.282, A:K.282, A:R.294, A:R.294, A:K.500, A:K.500, A:K.500

14 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 5 residues within 4Å: Chain A: I.396, Y.397, T.420, R.421, C.424 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.420, A:T.420, A:R.421 Water bridges: A:N.307, A:I.396 EDO.6: 7 residues within 4Å: Chain A: N.151, Q.152, I.153, L.279, L.406, N.407 Chain B: U.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.279, A:N.407, A:N.407 Water bridges: A:L.279 EDO.7: 5 residues within 4Å: Chain A: K.682, P.683, F.715, W.726, R.791 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.791, A:R.791 EDO.8: 8 residues within 4Å: Chain A: K.232, S.233, P.234, G.235, L.298, M.299, K.304 Chain B: A.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.299, A:M.299 EDO.9: 6 residues within 4Å: Chain A: I.349, N.350, K.355, Y.506, D.539 Ligands: EDO.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.350, A:K.355, A:D.539 EDO.10: 5 residues within 4Å: Chain A: N.350, R.351, A.352, K.355 Ligands: EDO.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.355, A:K.355 EDO.12: 8 residues within 4Å: Chain A: H.324, D.325, V.327, F.337, N.338, I.659, Q.661, W.662 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.338, A:Q.661, A:W.662 EDO.13: 3 residues within 4Å: Chain A: R.285, D.286, N.292 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.286, A:N.292 EDO.15: 5 residues within 4Å: Chain A: Q.655, A.804, T.805, S.807 Ligands: DIO.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.655 Water bridges: A:Y.654 EDO.17: 6 residues within 4Å: Chain A: L.505, Y.506, T.507, N.509, E.513, R.538 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.505, A:T.507, A:R.538 EDO.18: 4 residues within 4Å: Chain A: K.319, G.332, R.657, I.659 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.319, A:K.319, A:R.657 Water bridges: A:G.332, A:R.657 EDO.19: 7 residues within 4Å: Chain A: G.533, I.534, Q.535, E.546, P.550, E.554, R.587 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.533, A:Q.535, A:R.587, A:R.587 EDO.20: 4 residues within 4Å: Chain A: D.769, K.770, I.771, K.773 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.769, A:K.773 EDO.24: 4 residues within 4Å: Chain A: Q.315, P.331 Chain B: A.6, A.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.315

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.5: 6 residues within 4Å: Chain A: L.716, W.726, F.782, E.787, T.788, R.791 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.788 DMS.11: 7 residues within 4Å: Chain A: Y.675, N.676, P.683, E.684, N.686, W.700, R.725 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.684, A:R.725 pi-Cation interactions: A:W.700, A:W.700

1 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)

DIO.16: 5 residues within 4Å: Chain A: Y.654, Q.655, K.721, I.746 Ligands: EDO.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.655

2 x MG: MAGNESIUM ION(Non-covalent)

MG.21: 5 residues within 4Å: Chain A: K.319, I.322, H.323, H.324 Ligands: CIT.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:K.319, A:I.322, H2O.7 MG.22: 4 residues within 4Å: Chain A: D.363, A.364, D.465 Ligands: TTP.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.363, A:A.364, A:D.465

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.23: 4 residues within 4Å: Chain A: T.736, K.770, I.771, D.772 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baldwin, E.T. et al., Structures, functions and adaptations of the human LINE-1 ORF2 protein. Nature (2024)

Release Date

2023-12-20

Peptides

RNA-directed DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RNA-directed DNA polymerase