SMTL ID : 8q4d.1

IstA-IstB(E167Q) Strand Transfer Complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-20-mer

Ligands

20 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain 0: T.58 Chain 1: G.56 Chain A: D.124, W.125, D.187, K.229 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.124, A:D.187 MG.2: 6 residues within 4Å: Chain 3: T.58 Chain B: D.124, W.125, D.187, K.229 Chain Y: G.56 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.124, B:D.187 MG.4: 5 residues within 4Å: Chain F: K.112, T.113, D.167, T.198 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.113 MG.6: 4 residues within 4Å: Chain E: R.222 Chain G: K.112, T.113 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.113 MG.8: 6 residues within 4Å: Chain H: K.112, T.113, D.167, T.198 Chain J: R.222 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:T.113 MG.10: 4 residues within 4Å: Chain I: K.112, T.113, T.198 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:T.113 MG.12: 6 residues within 4Å: Chain J: K.112, T.113, D.167, Y.171, T.198 Ligands: ATP.13 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:T.113 MG.14: 5 residues within 4Å: Chain K: K.112, T.113, D.167, T.198 Ligands: ATP.15 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:T.113 MG.16: 6 residues within 4Å: Chain L: K.112, T.113, D.167, Y.171, T.198 Ligands: ATP.17 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:T.113 MG.18: 5 residues within 4Å: Chain M: K.112, T.113, D.167, T.198 Ligands: ATP.19 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:T.113 MG.20: 3 residues within 4Å: Chain N: K.112, T.113 Ligands: ATP.21 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:T.113 MG.23: 5 residues within 4Å: Chain P: K.112, T.113, D.167, T.198 Ligands: ATP.24 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:T.113 MG.25: 4 residues within 4Å: Chain O: R.222 Chain Q: K.112, T.113 Ligands: ATP.26 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:T.113 MG.27: 6 residues within 4Å: Chain R: K.112, T.113, D.167, T.198 Chain T: R.222 Ligands: ATP.28 1 PLIP interactions: 1 interactions with chain R Metal complexes: R:T.113 MG.29: 4 residues within 4Å: Chain S: K.112, T.113, T.198 Ligands: ATP.30 1 PLIP interactions: 1 interactions with chain S Metal complexes: S:T.113 MG.31: 6 residues within 4Å: Chain T: K.112, T.113, D.167, Y.171, T.198 Ligands: ATP.32 1 PLIP interactions: 1 interactions with chain T Metal complexes: T:T.113 MG.33: 5 residues within 4Å: Chain U: K.112, T.113, D.167, T.198 Ligands: ATP.34 1 PLIP interactions: 1 interactions with chain U Metal complexes: U:T.113 MG.35: 6 residues within 4Å: Chain V: K.112, T.113, D.167, Y.171, T.198 Ligands: ATP.36 1 PLIP interactions: 1 interactions with chain V Metal complexes: V:T.113 MG.37: 5 residues within 4Å: Chain W: K.112, T.113, D.167, T.198 Ligands: ATP.38 1 PLIP interactions: 1 interactions with chain W Metal complexes: W:T.113 MG.39: 3 residues within 4Å: Chain X: K.112, T.113 Ligands: ATP.40 1 PLIP interactions: 1 interactions with chain X Metal complexes: X:T.113

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.3: 17 residues within 4Å: Chain A: E.209, Y.213 Chain E: K.69, T.73, F.74, D.75, A.78, Q.79, P.108, G.109, I.110, G.111, K.112, T.113, H.114, Y.237, R.238 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:D.75, E:D.75, E:G.109, E:G.111, E:K.112, E:T.113, E:T.113 Salt bridges: E:K.112, E:K.112 pi-Stacking: E:H.114, E:Y.237, E:Y.237 ADP.22: 17 residues within 4Å: Chain B: E.209, Y.213 Chain O: K.69, T.73, F.74, D.75, A.78, Q.79, P.108, G.109, I.110, G.111, K.112, T.113, H.114, Y.237, R.238 12 PLIP interactions: 12 interactions with chain O Hydrogen bonds: O:D.75, O:D.75, O:G.109, O:G.111, O:K.112, O:T.113, O:T.113 Salt bridges: O:K.112, O:K.112 pi-Stacking: O:H.114, O:Y.237, O:Y.237

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

ATP.5: 21 residues within 4Å: Chain F: K.69, T.73, F.74, D.75, F.76, A.78, Q.79, P.108, G.109, I.110, G.111, K.112, T.113, H.114, Y.171, Y.237, R.238 Chain H: Y.190, R.222, H.225 Ligands: MG.4 17 PLIP interactions: 16 interactions with chain F, 1 interactions with chain H Hydrogen bonds: F:D.75, F:D.75, F:G.109, F:G.111, F:K.112, F:T.113, F:H.114, F:H.114 Salt bridges: F:K.69, F:K.112, F:K.112, F:R.238, F:R.238, F:R.238, H:R.222 pi-Stacking: F:Y.237 pi-Cation interactions: F:H.114 ATP.7: 23 residues within 4Å: Chain E: Y.190, R.222, H.225 Chain G: K.69, T.73, F.74, D.75, F.76, A.78, Q.79, P.107, P.108, G.109, I.110, G.111, K.112, T.113, H.114, Q.168, Y.171, Y.237, R.238 Ligands: MG.6 20 PLIP interactions: 19 interactions with chain G, 1 interactions with chain E Hydrogen bonds: G:D.75, G:D.75, G:G.109, G:I.110, G:G.111, G:K.112, G:T.113, G:T.113, G:H.114, G:H.114, G:Y.171, G:Y.171 Salt bridges: G:K.69, G:K.112, G:K.112, G:R.238, G:R.238, E:R.222 pi-Stacking: G:Y.237, G:Y.237 ATP.9: 20 residues within 4Å: Chain H: K.69, T.73, F.74, D.75, A.78, P.107, P.108, G.109, I.110, G.111, K.112, T.113, H.114, Y.171, Y.237, R.238 Chain J: Y.190, R.222, H.225 Ligands: MG.8 22 PLIP interactions: 20 interactions with chain H, 2 interactions with chain J Hydrogen bonds: H:K.69, H:D.75, H:D.75, H:G.109, H:I.110, H:G.111, H:K.112, H:T.113, H:T.113, H:H.114, H:H.114, H:Y.171, J:Y.190 Salt bridges: H:K.112, H:K.112, H:R.238, H:R.238, H:R.238, J:R.222 pi-Stacking: H:H.114, H:Y.237, H:Y.237 ATP.11: 21 residues within 4Å: Chain G: Y.190, R.222 Chain I: K.69, F.74, D.75, F.76, A.78, Q.79, P.107, P.108, G.109, I.110, G.111, K.112, T.113, H.114, Q.168, Y.171, Y.237, R.238 Ligands: MG.10 20 PLIP interactions: 19 interactions with chain I, 1 interactions with chain G Hydrogen bonds: I:D.75, I:D.75, I:G.109, I:I.110, I:G.111, I:K.112, I:T.113, I:H.114, I:Y.171, I:Y.171, I:Y.171 Salt bridges: I:K.69, I:K.112, I:K.112, I:R.238, I:R.238, I:R.238, G:R.222 pi-Stacking: I:Y.237 pi-Cation interactions: I:H.114 ATP.13: 21 residues within 4Å: Chain J: Y.67, K.69, T.73, F.74, D.75, F.76, A.78, Q.79, P.108, G.109, I.110, G.111, K.112, T.113, H.114, Q.168, Y.171, Y.237, R.238 Chain L: R.222 Ligands: MG.12 22 PLIP interactions: 21 interactions with chain J, 1 interactions with chain L Hydrogen bonds: J:K.69, J:D.75, J:D.75, J:G.109, J:G.111, J:K.112, J:T.113, J:T.113, J:H.114, J:H.114, J:Y.171, J:Y.171 Salt bridges: J:K.69, J:K.112, J:K.112, J:R.238, J:R.238, J:R.238, L:R.222 pi-Stacking: J:H.114, J:Y.237, J:Y.237 ATP.15: 19 residues within 4Å: Chain I: Y.190, R.222, H.225 Chain K: K.69, T.73, F.74, D.75, P.107, P.108, G.109, I.110, G.111, K.112, T.113, H.114, Y.171, Y.237, R.238 Ligands: MG.14 25 PLIP interactions: 24 interactions with chain K, 1 interactions with chain I Hydrogen bonds: K:K.69, K:D.75, K:D.75, K:G.109, K:I.110, K:G.111, K:K.112, K:T.113, K:H.114, K:H.114, K:Y.171, K:Y.171, K:Y.171, K:Y.237 Salt bridges: K:K.69, K:K.112, K:K.112, K:R.238, K:R.238, K:R.238, I:R.222 pi-Stacking: K:Y.237, K:Y.237 pi-Cation interactions: K:H.114, K:H.114 ATP.17: 20 residues within 4Å: Chain L: K.69, T.73, F.74, D.75, A.78, Q.79, P.108, G.109, I.110, G.111, K.112, T.113, H.114, Y.171, Y.237, R.238 Chain N: Y.190, R.222, H.225 Ligands: MG.16 24 PLIP interactions: 23 interactions with chain L, 1 interactions with chain N Hydrogen bonds: L:K.69, L:D.75, L:D.75, L:G.109, L:I.110, L:G.111, L:K.112, L:T.113, L:T.113, L:H.114, L:H.114, L:Y.171, L:Y.171 Salt bridges: L:K.69, L:K.112, L:K.112, L:R.238, L:R.238, L:R.238, N:R.222 pi-Stacking: L:H.114, L:H.114, L:Y.237, L:Y.237 ATP.19: 19 residues within 4Å: Chain K: Y.190, R.222, H.225 Chain M: K.69, T.73, F.74, D.75, P.107, P.108, G.109, I.110, G.111, K.112, T.113, H.114, Y.171, Y.237, R.238 Ligands: MG.18 23 PLIP interactions: 22 interactions with chain M, 1 interactions with chain K Hydrogen bonds: M:K.69, M:D.75, M:D.75, M:G.109, M:I.110, M:G.111, M:K.112, M:T.113, M:T.113, M:H.114, M:H.114, M:Y.171, M:Y.171 Salt bridges: M:K.69, M:K.112, M:K.112, M:R.238, M:R.238, M:R.238, K:R.222 pi-Stacking: M:Y.237, M:Y.237 pi-Cation interactions: M:H.114 ATP.21: 17 residues within 4Å: Chain N: Y.67, K.69, F.74, D.75, A.78, P.108, G.109, I.110, G.111, K.112, T.113, H.114, Y.171, Y.237, R.238, E.241 Ligands: MG.20 20 PLIP interactions: 20 interactions with chain N Hydrogen bonds: N:D.75, N:D.75, N:G.109, N:I.110, N:G.111, N:K.112, N:T.113, N:T.113, N:H.114, N:Y.171, N:Y.171 Salt bridges: N:K.69, N:K.112, N:K.112, N:R.238, N:R.238, N:R.238 pi-Stacking: N:Y.237, N:Y.237 pi-Cation interactions: N:H.114 ATP.24: 21 residues within 4Å: Chain P: K.69, T.73, F.74, D.75, F.76, A.78, Q.79, P.108, G.109, I.110, G.111, K.112, T.113, H.114, Y.171, Y.237, R.238 Chain R: Y.190, R.222, H.225 Ligands: MG.23 17 PLIP interactions: 1 interactions with chain R, 16 interactions with chain P Salt bridges: R:R.222, P:K.69, P:K.112, P:K.112, P:R.238, P:R.238, P:R.238 Hydrogen bonds: P:D.75, P:D.75, P:G.109, P:G.111, P:K.112, P:T.113, P:H.114, P:H.114 pi-Stacking: P:Y.237 pi-Cation interactions: P:H.114 ATP.26: 23 residues within 4Å: Chain O: Y.190, R.222, H.225 Chain Q: K.69, T.73, F.74, D.75, F.76, A.78, Q.79, P.107, P.108, G.109, I.110, G.111, K.112, T.113, H.114, Q.168, Y.171, Y.237, R.238 Ligands: MG.25 20 PLIP interactions: 19 interactions with chain Q, 1 interactions with chain O Hydrogen bonds: Q:D.75, Q:D.75, Q:G.109, Q:I.110, Q:G.111, Q:K.112, Q:T.113, Q:T.113, Q:H.114, Q:H.114, Q:Y.171, Q:Y.171 Salt bridges: Q:K.69, Q:K.112, Q:K.112, Q:R.238, Q:R.238, O:R.222 pi-Stacking: Q:Y.237, Q:Y.237 ATP.28: 20 residues within 4Å: Chain R: K.69, T.73, F.74, D.75, A.78, P.107, P.108, G.109, I.110, G.111, K.112, T.113, H.114, Y.171, Y.237, R.238 Chain T: Y.190, R.222, H.225 Ligands: MG.27 22 PLIP interactions: 20 interactions with chain R, 2 interactions with chain T Hydrogen bonds: R:K.69, R:D.75, R:D.75, R:G.109, R:I.110, R:G.111, R:K.112, R:T.113, R:T.113, R:H.114, R:H.114, R:Y.171, T:Y.190 Salt bridges: R:K.112, R:K.112, R:R.238, R:R.238, R:R.238, T:R.222 pi-Stacking: R:H.114, R:Y.237, R:Y.237 ATP.30: 21 residues within 4Å: Chain Q: Y.190, R.222 Chain S: K.69, F.74, D.75, F.76, A.78, Q.79, P.107, P.108, G.109, I.110, G.111, K.112, T.113, H.114, Q.168, Y.171, Y.237, R.238 Ligands: MG.29 20 PLIP interactions: 19 interactions with chain S, 1 interactions with chain Q Hydrogen bonds: S:D.75, S:D.75, S:G.109, S:I.110, S:G.111, S:K.112, S:T.113, S:H.114, S:Y.171, S:Y.171, S:Y.171 Salt bridges: S:K.69, S:K.112, S:K.112, S:R.238, S:R.238, S:R.238, Q:R.222 pi-Stacking: S:Y.237 pi-Cation interactions: S:H.114 ATP.32: 21 residues within 4Å: Chain T: Y.67, K.69, T.73, F.74, D.75, F.76, A.78, Q.79, P.108, G.109, I.110, G.111, K.112, T.113, H.114, Q.168, Y.171, Y.237, R.238 Chain V: R.222 Ligands: MG.31 22 PLIP interactions: 21 interactions with chain T, 1 interactions with chain V Hydrogen bonds: T:K.69, T:D.75, T:D.75, T:G.109, T:G.111, T:K.112, T:T.113, T:T.113, T:H.114, T:H.114, T:Y.171, T:Y.171 Salt bridges: T:K.69, T:K.112, T:K.112, T:R.238, T:R.238, T:R.238, V:R.222 pi-Stacking: T:H.114, T:Y.237, T:Y.237 ATP.34: 19 residues within 4Å: Chain S: Y.190, R.222, H.225 Chain U: K.69, T.73, F.74, D.75, P.107, P.108, G.109, I.110, G.111, K.112, T.113, H.114, Y.171, Y.237, R.238 Ligands: MG.33 25 PLIP interactions: 24 interactions with chain U, 1 interactions with chain S Hydrogen bonds: U:K.69, U:D.75, U:D.75, U:G.109, U:I.110, U:G.111, U:K.112, U:T.113, U:H.114, U:H.114, U:Y.171, U:Y.171, U:Y.171, U:Y.237 Salt bridges: U:K.69, U:K.112, U:K.112, U:R.238, U:R.238, U:R.238, S:R.222 pi-Stacking: U:Y.237, U:Y.237 pi-Cation interactions: U:H.114, U:H.114 ATP.36: 20 residues within 4Å: Chain V: K.69, T.73, F.74, D.75, A.78, Q.79, P.108, G.109, I.110, G.111, K.112, T.113, H.114, Y.171, Y.237, R.238 Chain X: Y.190, R.222, H.225 Ligands: MG.35 24 PLIP interactions: 23 interactions with chain V, 1 interactions with chain X Hydrogen bonds: V:K.69, V:D.75, V:D.75, V:G.109, V:I.110, V:G.111, V:K.112, V:T.113, V:T.113, V:H.114, V:H.114, V:Y.171, V:Y.171 Salt bridges: V:K.69, V:K.112, V:K.112, V:R.238, V:R.238, V:R.238, X:R.222 pi-Stacking: V:H.114, V:H.114, V:Y.237, V:Y.237 ATP.38: 19 residues within 4Å: Chain U: Y.190, R.222, H.225 Chain W: K.69, T.73, F.74, D.75, P.107, P.108, G.109, I.110, G.111, K.112, T.113, H.114, Y.171, Y.237, R.238 Ligands: MG.37 23 PLIP interactions: 22 interactions with chain W, 1 interactions with chain U Hydrogen bonds: W:K.69, W:D.75, W:D.75, W:G.109, W:I.110, W:G.111, W:K.112, W:T.113, W:T.113, W:H.114, W:H.114, W:Y.171, W:Y.171 Salt bridges: W:K.69, W:K.112, W:K.112, W:R.238, W:R.238, W:R.238, U:R.222 pi-Stacking: W:Y.237, W:Y.237 pi-Cation interactions: W:H.114 ATP.40: 17 residues within 4Å: Chain X: Y.67, K.69, F.74, D.75, A.78, P.108, G.109, I.110, G.111, K.112, T.113, H.114, Y.171, Y.237, R.238, E.241 Ligands: MG.39 20 PLIP interactions: 20 interactions with chain X Hydrogen bonds: X:D.75, X:D.75, X:G.109, X:I.110, X:G.111, X:K.112, X:T.113, X:T.113, X:H.114, X:Y.171, X:Y.171 Salt bridges: X:K.69, X:K.112, X:K.112, X:R.238, X:R.238, X:R.238 pi-Stacking: X:Y.237, X:Y.237 pi-Cation interactions: X:H.114

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

Putative transposase for insertion sequence element IS5376: ABCD
Insertion sequence IS5376 putative ATP-binding protein: EFGHIJKLMNOPQRSTUVWX

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

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
R

S
S

T
T

U
U

V
V

W
W

X
X

Putative transposase for insertion sequence element IS5376

Insertion sequence IS5376 putative ATP-binding protein