SMTL ID : 8v32.1

TnsD-TnsC-DNA complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-7-1-mer

Ligands

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

ATP.1: 18 residues within 4Å: Chain A: Y.26, T.27, V.28, H.30, A.58, S.59, G.60, V.61, G.62, K.63, T.64, T.65, E.172, G.279, K.282 Chain B: Q.220, R.224 Ligands: MG.2 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:V.28, A:V.28, A:A.58, A:G.60, A:V.61, A:G.62, A:K.63, A:T.64, B:Q.220, B:Q.220 Salt bridges: A:K.63, A:K.63, B:R.223, B:R.224 ATP.3: 21 residues within 4Å: Chain B: Y.26, T.27, V.28, H.30, L.33, A.58, S.59, G.60, V.61, G.62, K.63, T.64, T.65, T.208, G.279, K.282, D.283 Chain C: Q.220, R.223, R.224 Ligands: MG.4 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:V.28, B:V.28, B:A.58, B:G.60, B:V.61, B:G.62, B:K.63, B:T.64, B:T.64, B:T.65, B:D.283 Salt bridges: B:K.63, B:K.63, C:R.223, C:R.224 ATP.5: 22 residues within 4Å: Chain C: Y.26, T.27, V.28, H.30, L.33, A.58, S.59, G.60, V.61, G.62, K.63, T.64, T.65, E.172, T.208, G.279, K.282, D.283 Chain D: Q.220, R.223, R.224 Ligands: MG.6 17 PLIP interactions: 12 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:V.28, C:V.28, C:A.58, C:S.59, C:G.60, C:V.61, C:G.62, C:K.63, C:T.64, C:T.65, D:Q.220, D:Q.220 Salt bridges: C:K.63, C:K.63, D:R.223, D:R.223, D:R.224 ATP.7: 23 residues within 4Å: Chain D: E.24, Y.26, T.27, V.28, H.30, L.33, A.58, S.59, G.60, V.61, G.62, K.63, T.64, T.65, E.172, T.208, I.278, G.279, K.282 Chain E: Q.220, R.223, R.224 Ligands: MG.8 15 PLIP interactions: 12 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:V.28, D:V.28, D:G.60, D:V.61, D:G.62, D:K.63, D:T.64, D:T.64, D:T.65, D:K.282, E:Q.220 Salt bridges: D:K.63, D:K.63, E:R.223, E:R.224 ATP.9: 20 residues within 4Å: Chain E: T.27, V.28, H.30, L.33, S.59, G.60, V.61, G.62, K.63, T.64, T.65, E.172, T.208, I.278, G.279, K.282 Chain F: Q.220, R.223, R.224 Ligands: MG.10 14 PLIP interactions: 10 interactions with chain E, 4 interactions with chain F Hydrogen bonds: E:V.28, E:V.28, E:S.59, E:G.60, E:G.62, E:K.63, E:T.64, E:T.65, F:Q.220 Salt bridges: E:K.63, E:K.63, F:R.223, F:R.223, F:R.224 ATP.11: 20 residues within 4Å: Chain F: Y.26, T.27, V.28, H.30, L.33, A.58, S.59, G.60, V.61, G.62, K.63, T.64, T.65, T.208, G.279, K.282 Chain G: Q.220, R.223, R.224 Ligands: MG.12 16 PLIP interactions: 5 interactions with chain G, 11 interactions with chain F Hydrogen bonds: G:Q.220, F:V.28, F:V.28, F:G.60, F:V.61, F:G.62, F:K.63, F:T.64, F:T.65, F:T.65 Salt bridges: G:R.223, G:R.223, G:R.223, G:R.224, F:K.63, F:K.63 ATP.13: 15 residues within 4Å: Chain G: Y.26, T.27, V.28, A.58, S.59, G.60, V.61, G.62, K.63, T.64, T.65, G.279, K.282, D.283 Ligands: MG.14 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:T.27, G:V.28, G:V.28, G:G.60, G:V.61, G:G.62, G:K.63, G:T.64, G:T.65, G:K.282 Salt bridges: G:K.63, G:K.63

7 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.64, D.171 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.64 MG.4: 3 residues within 4Å: Chain B: T.64, D.171 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.64 MG.6: 2 residues within 4Å: Chain C: T.64 Ligands: ATP.5 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:T.64, H2O.1 MG.8: 2 residues within 4Å: Chain D: T.64 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.64 MG.10: 3 residues within 4Å: Chain E: T.64, D.171 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.64 MG.12: 2 residues within 4Å: Chain F: T.64 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.64 MG.14: 3 residues within 4Å: Chain G: T.64, D.171 Ligands: ATP.13 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.15: 4 residues within 4Å: Chain J: C.139, C.142, C.167, H.170 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.139, J:C.142, J:C.167, J:H.170 ZN.16: 4 residues within 4Å: Chain J: C.178, C.181, C.197, C.200 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.178, J:C.181, J:C.197, J:C.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, S. et al., Structure of TnsABCD transpososome reveals mechanisms of targeted DNA transposition. Cell (2024)

Release Date

2024-10-16

Peptides

TnsC: ABCDEFG
TnsD: J

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
Q

B
R

C
S

D
T

E
U

F
V

G
W

J
J

TnsC

TnsD

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