SMTL ID : 8bd4.1

TniQ-capped Tns-ATP-dsDNA complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-7-3-mer

Ligands

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

ATP.1: 22 residues within 4Å: Chain A: K.31, S.32, I.33, V.34, V.39, S.62, R.63, T.64, G.65, K.66, T.67, V.68, E.145, T.173, W.211, I.241, G.242, D.245 Chain B: E.162, Q.185, R.189 Ligands: MG.2 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.31, A:K.31, A:V.34, A:V.34, A:R.63, A:T.64, A:G.65, A:K.66, A:T.67, A:T.67, A:V.68, A:E.145 Salt bridges: A:K.66, A:K.66, B:R.189 ATP.4: 21 residues within 4Å: Chain B: K.31, S.32, I.33, V.34, V.39, S.62, R.63, T.64, G.65, K.66, T.67, V.68, E.145, T.173, W.211, I.241, G.242, D.245 Chain C: E.162, R.189 Ligands: MG.5 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:K.31, B:K.31, B:V.34, B:V.34, B:R.63, B:T.64, B:G.65, B:K.66, B:T.67, B:T.67, B:V.68, B:E.145 Salt bridges: B:K.66, B:K.66, C:R.189 ATP.6: 21 residues within 4Å: Chain C: K.31, S.32, I.33, V.34, V.39, S.62, R.63, T.64, G.65, K.66, T.67, V.68, E.145, T.173, W.211, I.241, G.242, D.245 Chain D: E.162, R.189 Ligands: MG.7 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:K.31, C:K.31, C:V.34, C:V.34, C:R.63, C:T.64, C:G.65, C:K.66, C:T.67, C:T.67, C:V.68, C:E.145 Salt bridges: C:K.66, C:K.66, D:R.189 ATP.8: 21 residues within 4Å: Chain D: K.31, S.32, I.33, V.34, V.39, S.62, R.63, T.64, G.65, K.66, T.67, V.68, E.145, T.173, W.211, I.241, G.242, D.245 Chain E: E.162, R.189 Ligands: MG.9 15 PLIP interactions: 14 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:K.31, D:K.31, D:V.34, D:V.34, D:R.63, D:T.64, D:G.65, D:K.66, D:T.67, D:T.67, D:V.68, D:E.145 Salt bridges: D:K.66, D:K.66, E:R.189 ATP.10: 22 residues within 4Å: Chain E: K.31, S.32, I.33, V.34, V.39, S.62, R.63, T.64, G.65, K.66, T.67, V.68, E.145, T.173, W.211, I.241, G.242, D.245 Chain F: E.162, Q.185, R.189 Ligands: MG.11 15 PLIP interactions: 14 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:K.31, E:K.31, E:V.34, E:V.34, E:R.63, E:T.64, E:G.65, E:K.66, E:T.67, E:T.67, E:V.68, E:E.145 Salt bridges: E:K.66, E:K.66, F:R.189 ATP.13: 22 residues within 4Å: Chain F: K.31, S.32, I.33, V.34, V.39, S.62, R.63, T.64, G.65, K.66, T.67, V.68, E.145, T.173, W.211, I.241, G.242, D.245 Chain G: E.162, Q.185, R.189 Ligands: MG.14 15 PLIP interactions: 14 interactions with chain F, 1 interactions with chain G Hydrogen bonds: F:K.31, F:K.31, F:V.34, F:V.34, F:R.63, F:T.64, F:G.65, F:K.66, F:T.67, F:T.67, F:V.68, F:E.145 Salt bridges: F:K.66, F:K.66, G:R.189 ATP.15: 19 residues within 4Å: Chain G: K.31, S.32, I.33, V.34, V.39, S.62, R.63, T.64, G.65, K.66, T.67, V.68, E.145, T.173, W.211, I.241, G.242, D.245 Ligands: MG.16 15 PLIP interactions: 15 interactions with chain G Hydrogen bonds: G:K.31, G:K.31, G:V.34, G:V.34, G:R.63, G:T.64, G:G.65, G:K.66, G:T.67, G:T.67, G:V.68, G:E.145, G:E.145 Salt bridges: G:K.66, G:K.66

7 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.67 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.67 MG.5: 2 residues within 4Å: Chain B: T.67 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.67 MG.7: 2 residues within 4Å: Chain C: T.67 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.67 MG.9: 2 residues within 4Å: Chain D: T.67 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.67 MG.11: 2 residues within 4Å: Chain E: T.67 Ligands: ATP.10 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.67 MG.14: 2 residues within 4Å: Chain F: T.67 Ligands: ATP.13 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.67 MG.16: 2 residues within 4Å: Chain G: T.67 Ligands: ATP.15 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.67

6 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain A: R.128, E.131 Chain I: C.133, C.136, C.151, C.154 5 PLIP interactions: 4 interactions with chain I, 1 interactions with chain A Metal complexes: I:C.133, I:C.136, I:C.151, I:C.154, A:E.131 ZN.12: 6 residues within 4Å: Chain E: R.128, E.131 Chain H: C.133, C.136, C.151, C.154 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.133, H:C.136, H:C.151, H:C.154 ZN.17: 4 residues within 4Å: Chain H: C.100, C.103, C.122, H.125 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.100, H:C.103, H:C.122, H:H.125 ZN.18: 4 residues within 4Å: Chain I: C.100, C.103, C.122, H.125 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.100, I:C.103, I:C.122, I:H.125 ZN.19: 6 residues within 4Å: Chain C: R.128, E.131 Chain J: C.133, C.136, C.151, C.154 5 PLIP interactions: 4 interactions with chain J, 1 interactions with chain C Metal complexes: J:C.133, J:C.136, J:C.151, J:C.154, C:E.131 ZN.20: 4 residues within 4Å: Chain J: C.100, C.103, C.122, H.125 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.100, J:C.103, J:C.122, J:H.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schmitz, M. et al., Structural basis for the assembly of the type V CRISPR-associated transposon complex. Cell (2022)

Release Date

2022-12-28

Peptides

TnsC: ABCDEFG
TniQ (Homology model): HIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
R

I
S

J
T

TnsC

TniQ (Homology model)

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