SMTL ID : 9bw1.1

TnsABCD-DNA transpososome

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-8-9-mer

Ligands

11 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain B: A.158, T.160 Chain I: T.521, E.522, D.524, N.631 No protein-ligand interaction detected (PLIP) MG.2: 3 residues within 4Å: Chain F: A.70, G.72 Chain H: D.524 No protein-ligand interaction detected (PLIP) MG.3: 5 residues within 4Å: Chain D: A.37 Chain F: A.70, C.71 Chain H: H.520, T.521 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:H.520 MG.6: 3 residues within 4Å: Chain A: A.13 Chain H: E.57, D.104 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:D.104 MG.8: 2 residues within 4Å: Chain L: T.64 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:T.64 MG.10: 3 residues within 4Å: Chain M: T.64, E.172 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:T.64 MG.12: 5 residues within 4Å: Chain N: T.64, D.171, E.172 Chain O: R.224 Ligands: ATP.11 4 PLIP interactions: 1 interactions with chain N, 3 Ligand-Water interactions Metal complexes: N:T.64, H2O.1, H2O.1, H2O.1 MG.14: 3 residues within 4Å: Chain O: T.64, E.172 Ligands: ATP.13 No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Chain P: T.64 Ligands: ATP.15 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:T.64 MG.18: 2 residues within 4Å: Chain Q: T.64 Ligands: ATP.17 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:T.64 MG.20: 2 residues within 4Å: Chain R: T.64 Ligands: ATP.19 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain G: C.139, C.142, C.167, H.170 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.139, G:C.142, G:C.167, G:H.170 ZN.5: 4 residues within 4Å: Chain G: C.178, C.181, C.197, C.200 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.178, G:C.181, G:C.197, G:C.200

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

ATP.7: 21 residues within 4Å: Chain L: 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 Chain M: Q.220, R.223, R.224 Ligands: MG.8 19 PLIP interactions: 14 interactions with chain L, 5 interactions with chain M Hydrogen bonds: L:T.27, L:V.28, L:V.28, L:A.58, L:G.60, L:V.61, L:G.62, L:K.63, L:T.64, L:T.65, L:T.65, L:K.282, M:Q.220 Salt bridges: L:K.63, L:K.63, M:R.223, M:R.223, M:R.223, M:R.224 ATP.9: 18 residues within 4Å: Chain M: T.27, V.28, H.30, L.33, A.58, V.61, G.62, K.63, T.64, T.65, E.172, T.208, G.279, K.282 Chain N: Q.220, R.223, R.224 Ligands: MG.10 16 PLIP interactions: 12 interactions with chain M, 4 interactions with chain N Hydrogen bonds: M:T.27, M:V.28, M:V.28, M:V.61, M:G.62, M:K.63, M:T.64, M:T.64, M:T.65, M:K.282, N:Q.220 Salt bridges: M:K.63, M:K.63, N:R.223, N:R.223, N:R.224 ATP.11: 24 residues within 4Å: Chain N: 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, F.251, I.278, G.279, K.282, D.283 Chain O: Q.220, R.223, R.224 Ligands: MG.12 22 PLIP interactions: 15 interactions with chain N, 7 interactions with chain O Hydrogen bonds: N:V.28, N:V.28, N:A.58, N:G.60, N:V.61, N:G.62, N:K.63, N:T.64, N:T.64, N:T.64, N:T.65, N:T.65, N:K.282, O:Q.220, O:Q.220 Salt bridges: N:K.63, N:K.63, O:R.224 Water bridges: O:R.223, O:R.224, O:R.224, O:R.224 ATP.13: 19 residues within 4Å: Chain O: Y.26, T.27, V.28, H.30, L.33, S.59, G.60, V.61, G.62, K.63, T.64, T.65, E.172, G.279, K.282 Chain P: Q.220, R.223, R.224 Ligands: MG.14 19 PLIP interactions: 16 interactions with chain O, 3 interactions with chain P Hydrogen bonds: O:T.27, O:V.28, O:V.28, O:G.60, O:V.61, O:G.62, O:K.63, O:T.64, O:T.64, O:T.64, O:T.65, O:E.172, O:E.172, O:K.282, P:Q.220 Salt bridges: O:K.63, O:K.63, P:R.223, P:R.224 ATP.15: 21 residues within 4Å: Chain P: 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, F.251, G.279, K.282 Chain Q: Q.220, R.223, R.224 Ligands: MG.16 20 PLIP interactions: 14 interactions with chain P, 6 interactions with chain Q Hydrogen bonds: P:V.28, P:V.28, P:H.30, P:V.61, P:G.62, P:K.63, P:T.64, P:T.64, P:T.64, P:T.65, P:T.65, P:K.282, Q:Q.220, Q:Q.220, Q:R.223 Salt bridges: P:K.63, P:K.63, Q:R.223, Q:R.223, Q:R.224 ATP.17: 21 residues within 4Å: Chain Q: Y.26, T.27, V.28, H.30, L.33, S.59, G.60, V.61, G.62, K.63, T.64, T.65, T.208, F.251, G.279, K.282, D.283 Chain R: Q.220, R.223, R.224 Ligands: MG.18 17 PLIP interactions: 5 interactions with chain R, 12 interactions with chain Q Hydrogen bonds: R:Q.220, Q:V.28, Q:V.28, Q:G.60, Q:V.61, Q:G.62, Q:K.63, Q:T.64, Q:T.64, Q:T.65, Q:T.65 Salt bridges: R:R.223, R:R.223, R:R.223, R:R.224, Q:K.63, Q:K.63 ATP.19: 19 residues within 4Å: Chain R: Y.26, T.27, V.28, L.33, A.58, S.59, G.60, V.61, G.62, K.63, T.64, T.65, D.171, T.208, G.279, K.282, D.283, K.286 Ligands: MG.20 15 PLIP interactions: 15 interactions with chain R Hydrogen bonds: R:T.27, R:V.28, R:V.28, R:A.58, R:G.60, R:V.61, R:G.62, R:K.63, R:T.64, R:T.65, R:T.208, R:K.282, R:D.283 Salt bridges: R:K.63, R:K.63

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

TnsD: G
Integrase: HIJKSTUV
TnsC: LMNOPQRWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

G
J

H
M

I
N

J
O

K
P

S
a

T
b

U
c

V
d

L
Q

M
R

N
S

O
T

P
U

Q
V

R
W

W
x

X
y

TnsD

Integrase

TnsC

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