SMTL ID : 8q3w.1

ATP-bound IstB in complex to duplex DNA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-10-mer

Ligands

10 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: T.115, R.240 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.115 MG.3: 6 residues within 4Å: Chain B: K.114, T.115, D.169, R.240 Chain D: R.224 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.115 MG.5: 5 residues within 4Å: Chain A: R.224 Chain C: T.115, D.169, E.170 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.115 MG.7: 5 residues within 4Å: Chain D: T.115, D.169, E.170 Chain F: R.224 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.115 MG.9: 6 residues within 4Å: Chain C: R.224 Chain E: T.115, D.169, E.170, R.240 Ligands: ATP.10 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.115 MG.11: 6 residues within 4Å: Chain F: T.115, D.169, E.170, R.240 Chain H: R.224 Ligands: ATP.12 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.115 MG.13: 5 residues within 4Å: Chain E: R.224 Chain G: T.115, D.169, E.170 Ligands: ATP.14 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.115 MG.15: 5 residues within 4Å: Chain H: T.115, D.169, E.170 Chain J: R.224 Ligands: ATP.16 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:T.115 MG.17: 6 residues within 4Å: Chain G: R.224 Chain I: K.114, T.115, D.169, R.240 Ligands: ATP.18 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:T.115 MG.19: 3 residues within 4Å: Chain J: T.115, R.240 Ligands: ATP.20 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:T.115

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

ATP.2: 20 residues within 4Å: Chain A: Y.69, K.71, T.75, F.76, D.77, A.80, Q.81, P.109, P.110, G.111, I.112, G.113, K.114, T.115, H.116, E.170, Y.173, Y.239, R.240 Ligands: MG.1 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:Y.69, A:D.77, A:D.77, A:G.111, A:I.112, A:G.113, A:K.114, A:T.115, A:T.115, A:H.116, A:H.116, A:E.170, A:Y.173, A:Y.173 Salt bridges: A:K.114, A:K.114, A:R.240, A:R.240, A:R.240 pi-Stacking: A:H.116, A:Y.239, A:Y.239 ATP.4: 25 residues within 4Å: Chain B: Y.69, K.71, T.75, F.76, D.77, A.80, Q.81, P.110, G.111, I.112, G.113, K.114, T.115, H.116, D.169, E.170, Y.173, Y.239, R.240, E.243 Chain D: Y.192, E.193, R.224, H.227 Ligands: MG.3 21 PLIP interactions: 20 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:Y.69, B:D.77, B:D.77, B:G.111, B:I.112, B:G.113, B:K.114, B:T.115, B:H.116, B:H.116, B:Y.173, B:Y.173 Salt bridges: B:K.114, B:K.114, B:R.240, B:R.240, B:R.240, D:R.224 pi-Stacking: B:H.116, B:Y.239, B:Y.239 ATP.6: 23 residues within 4Å: Chain A: Y.192, E.193, R.224, H.227 Chain C: Y.69, K.71, T.75, F.76, D.77, A.80, Q.81, P.110, G.111, I.112, G.113, K.114, T.115, H.116, E.170, Y.173, Y.239, R.240 Ligands: MG.5 23 PLIP interactions: 21 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:Y.69, C:Y.69, C:D.77, C:D.77, C:G.111, C:I.112, C:G.113, C:K.114, C:T.115, C:H.116, C:H.116, C:Y.173, C:Y.173, A:E.193 Salt bridges: C:K.114, C:K.114, C:R.240, C:R.240, C:R.240, A:R.224 pi-Stacking: C:H.116, C:Y.239, C:Y.239 ATP.8: 23 residues within 4Å: Chain D: Y.69, K.71, T.75, F.76, D.77, A.80, Q.81, P.109, P.110, G.111, I.112, G.113, K.114, T.115, H.116, E.170, Y.173, Y.239, R.240 Chain F: Y.192, R.224, H.227 Ligands: MG.7 21 PLIP interactions: 1 interactions with chain F, 20 interactions with chain D Salt bridges: F:R.224, D:K.114, D:K.114, D:R.240, D:R.240, D:R.240 Hydrogen bonds: D:K.71, D:D.77, D:D.77, D:G.111, D:I.112, D:G.113, D:K.114, D:T.115, D:H.116, D:H.116, D:Y.173, D:Y.173 pi-Stacking: D:H.116, D:Y.239, D:Y.239 ATP.10: 23 residues within 4Å: Chain C: Y.192, R.224, H.227 Chain E: Y.69, K.71, T.75, F.76, D.77, A.80, Q.81, P.109, P.110, G.111, I.112, G.113, K.114, T.115, H.116, E.170, Y.173, Y.239, R.240 Ligands: MG.9 22 PLIP interactions: 1 interactions with chain C, 21 interactions with chain E Salt bridges: C:R.224, E:K.114, E:K.114, E:R.240, E:R.240, E:R.240 Hydrogen bonds: E:K.71, E:D.77, E:D.77, E:G.111, E:I.112, E:G.113, E:K.114, E:T.115, E:H.116, E:H.116, E:Y.173, E:Y.173 pi-Stacking: E:H.116, E:H.116, E:Y.239, E:Y.239 ATP.12: 23 residues within 4Å: Chain F: Y.69, K.71, T.75, F.76, D.77, A.80, Q.81, P.109, P.110, G.111, I.112, G.113, K.114, T.115, H.116, E.170, Y.173, Y.239, R.240 Chain H: Y.192, R.224, H.227 Ligands: MG.11 22 PLIP interactions: 21 interactions with chain F, 1 interactions with chain H Hydrogen bonds: F:K.71, F:D.77, F:D.77, F:G.111, F:I.112, F:G.113, F:K.114, F:T.115, F:H.116, F:H.116, F:Y.173, F:Y.173 Salt bridges: F:K.114, F:K.114, F:R.240, F:R.240, F:R.240, H:R.224 pi-Stacking: F:H.116, F:H.116, F:Y.239, F:Y.239 ATP.14: 23 residues within 4Å: Chain E: Y.192, R.224, H.227 Chain G: Y.69, K.71, T.75, F.76, D.77, A.80, Q.81, P.109, P.110, G.111, I.112, G.113, K.114, T.115, H.116, E.170, Y.173, Y.239, R.240 Ligands: MG.13 21 PLIP interactions: 20 interactions with chain G, 1 interactions with chain E Hydrogen bonds: G:K.71, G:D.77, G:D.77, G:G.111, G:I.112, G:G.113, G:K.114, G:T.115, G:H.116, G:H.116, G:Y.173, G:Y.173 Salt bridges: G:K.114, G:K.114, G:R.240, G:R.240, G:R.240, E:R.224 pi-Stacking: G:H.116, G:Y.239, G:Y.239 ATP.16: 23 residues within 4Å: Chain H: Y.69, K.71, T.75, F.76, D.77, A.80, Q.81, P.110, G.111, I.112, G.113, K.114, T.115, H.116, E.170, Y.173, Y.239, R.240 Chain J: Y.192, E.193, R.224, H.227 Ligands: MG.15 23 PLIP interactions: 21 interactions with chain H, 2 interactions with chain J Hydrogen bonds: H:D.77, H:D.77, H:G.111, H:I.112, H:G.113, H:K.114, H:T.115, H:T.115, H:H.116, H:H.116, H:E.170, H:Y.173, H:Y.173, J:E.193 Salt bridges: H:K.114, H:K.114, H:R.240, H:R.240, H:R.240, J:R.224 pi-Stacking: H:H.116, H:Y.239, H:Y.239 ATP.18: 25 residues within 4Å: Chain G: Y.192, E.193, R.224, H.227 Chain I: Y.69, K.71, T.75, F.76, D.77, A.80, Q.81, P.110, G.111, I.112, G.113, K.114, T.115, H.116, D.169, E.170, Y.173, Y.239, R.240, E.243 Ligands: MG.17 21 PLIP interactions: 20 interactions with chain I, 1 interactions with chain G Hydrogen bonds: I:Y.69, I:D.77, I:D.77, I:G.111, I:I.112, I:G.113, I:K.114, I:T.115, I:H.116, I:H.116, I:Y.173, I:Y.173 Salt bridges: I:K.114, I:K.114, I:R.240, I:R.240, I:R.240, G:R.224 pi-Stacking: I:H.116, I:Y.239, I:Y.239 ATP.20: 20 residues within 4Å: Chain J: Y.69, K.71, T.75, F.76, D.77, A.80, Q.81, P.109, P.110, G.111, I.112, G.113, K.114, T.115, H.116, E.170, Y.173, Y.239, R.240 Ligands: MG.19 22 PLIP interactions: 22 interactions with chain J Hydrogen bonds: J:Y.69, J:D.77, J:D.77, J:G.111, J:I.112, J:G.113, J:K.114, J:T.115, J:T.115, J:H.116, J:H.116, J:E.170, J:Y.173, J:Y.173 Salt bridges: J:K.114, J:K.114, J:R.240, J:R.240, J:R.240 pi-Stacking: J:H.116, J:Y.239, J:Y.239

Links

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Citation

de la Gandara, A. et al., Molecular basis for transposase activation by a dedicated AAA+ ATPase. Nature (2024)

Release Date

2024-07-10

Peptides

Insertion sequence IS5376 putative ATP-binding protein: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

Insertion sequence IS5376 putative ATP-binding protein