SMTL ID : 8e2l.1

Structure of Lates calcarifer Twinkle helicase with ATP and DNA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

5 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 20 residues within 4Å: Chain A: T.297, G.298, S.299, G.300, K.301, T.302, T.303, Q.325, H.438, R.481, F.501, K.503, L.506, F.508 Chain D: Q.461, K.487, R.489, D.491, G.492 Ligands: MG.2 17 PLIP interactions: 11 interactions with chain A, 6 interactions with chain D Hydrogen bonds: A:G.298, A:G.300, A:K.301, A:T.302, A:T.302, A:T.303, A:Q.325, A:R.481, D:Q.461, D:R.489, D:D.491, D:G.492 Salt bridges: A:K.301, A:K.301, A:H.438, D:K.487, D:R.489 ATP.3: 19 residues within 4Å: Chain C: K.487, N.488, R.489, D.491, G.492 Chain D: G.298, S.299, G.300, K.301, T.302, T.303, Q.325, H.438, R.481, F.501, K.503, L.506, F.508 Ligands: MG.4 18 PLIP interactions: 13 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:G.298, D:G.300, D:K.301, D:T.302, D:T.302, D:T.303, D:Q.325, D:Q.325, C:R.489, C:D.491, C:G.492 Salt bridges: D:K.301, D:K.301, D:H.438, C:K.487, C:R.489 pi-Stacking: D:F.501, D:F.501 ATP.5: 15 residues within 4Å: Chain A: Q.461, K.487, R.489 Chain E: T.297, G.298, G.300, K.301, T.302, T.303, Q.325, R.481, F.501, L.506, F.508 Ligands: MG.6 17 PLIP interactions: 5 interactions with chain A, 12 interactions with chain E Hydrogen bonds: A:Q.461, A:R.489, A:D.491, E:G.298, E:G.300, E:K.301, E:T.302, E:T.302, E:T.302, E:T.303, E:Q.325, E:R.481 Salt bridges: A:K.487, A:R.489, E:K.301, E:K.301, E:H.438 ATP.7: 17 residues within 4Å: Chain E: Q.461, K.487, R.489 Chain F: G.298, S.299, G.300, K.301, T.302, T.303, Q.325, H.438, R.481, F.501, K.503, L.506, F.508 Ligands: MG.8 16 PLIP interactions: 12 interactions with chain F, 4 interactions with chain E Hydrogen bonds: F:G.298, F:G.300, F:K.301, F:T.302, F:T.302, F:T.303, F:T.303, F:Q.325, F:R.481, E:Q.461, E:R.489 Salt bridges: F:K.301, F:K.301, F:H.438, E:K.487, E:R.489 ATP.9: 19 residues within 4Å: Chain F: Q.461, K.487, N.488, R.489, D.491, G.492 Chain G: T.297, G.298, G.300, K.301, T.302, T.303, Q.325, H.438, R.481, F.501, K.503, F.508 Ligands: MG.10 19 PLIP interactions: 12 interactions with chain G, 7 interactions with chain F Hydrogen bonds: G:G.298, G:G.300, G:K.301, G:T.302, G:T.302, G:T.303, G:T.303, G:Q.325, G:R.481, F:Q.461, F:R.489, F:D.491, F:G.492 Salt bridges: G:K.301, G:K.301, G:H.438, F:K.487, F:R.489, F:R.489

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.302, Q.325, D.396 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.302 MG.4: 3 residues within 4Å: Chain D: T.302, Q.325 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.302 MG.6: 4 residues within 4Å: Chain E: T.302, Q.325, N.397 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.302 MG.8: 4 residues within 4Å: Chain F: T.302, Q.325, N.397 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.302 MG.10: 3 residues within 4Å: Chain G: T.302, Q.325 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.302

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Z. et al., Structural and dynamic basis of DNA capture and translocation by mitochondrial Twinkle helicase. Nucleic Acids Res. (2022)

Release Date

2022-11-02

Peptides

Twinkle mtDNA helicase: ACDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

C
A

D
B

E
D

F
E

G
F

Twinkle mtDNA helicase