SMTL ID : 8bd6.1

Cas12k-sgRNA-dsDNA-TnsC non-productive complex.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-9-mer

Ligands

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

ATP.1: 18 residues within 4Å: Chain E: K.31, S.32, I.33, V.34, S.62, R.63, T.64, G.65, K.66, T.67, V.68, W.211, I.241, G.242, D.245 Chain F: Q.185, R.189 Ligands: MG.2 16 PLIP interactions: 15 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:K.31, E:V.34, E:V.34, E:R.63, E:R.63, E:T.64, E:G.65, E:K.66, E:T.67, E:T.67, E:T.67, E:V.68, E:G.242, E:D.245 Salt bridges: E:K.66, F:R.189 ATP.3: 23 residues within 4Å: Chain F: K.31, S.32, V.34, L.36, E.61, 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: R.158, E.162, Q.185, R.189 Ligands: MG.4 20 PLIP interactions: 18 interactions with chain F, 2 interactions with chain G Hydrogen bonds: F:K.31, F:K.31, F:V.34, F:V.34, F:E.61, F:R.63, F:R.63, F:T.64, F:G.65, F:K.66, F:T.67, F:T.67, F:T.67, F:V.68, F:E.145, F:D.245 Salt bridges: F:K.66, F:K.66, G:R.158, G:R.189 ATP.5: 21 residues within 4Å: Chain G: K.31, S.32, I.33, V.34, V.39, E.61, S.62, R.63, T.64, G.65, K.66, T.67, V.68, T.173, W.211, I.241, G.242, D.245 Chain H: Q.185, R.189 Ligands: MG.6 15 PLIP interactions: 14 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:K.31, G:K.31, G:V.34, G:V.34, G:E.61, G:R.63, G:T.64, G:G.65, G:K.66, G:T.67, G:T.67, G:V.68, G:D.245 Salt bridges: G:K.66, H:R.189 ATP.7: 20 residues within 4Å: Chain H: K.31, S.32, E.61, 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 I: R.158, Q.185, R.189 Ligands: MG.8 20 PLIP interactions: 18 interactions with chain H, 2 interactions with chain I Hydrogen bonds: H:K.31, H:K.31, H:V.34, H:E.61, H:R.63, H:R.63, H:T.64, H:G.65, H:K.66, H:T.67, H:T.67, H:T.67, H:V.68, H:T.173, H:T.173, H:D.245, I:R.158, I:R.189 Salt bridges: H:K.66, H:K.66 ATP.9: 19 residues within 4Å: Chain I: K.31, S.32, I.33, V.34, E.61, S.62, R.63, T.64, G.65, K.66, T.67, V.68, T.173, W.211, G.242, D.245 Chain J: Q.185, R.189 Ligands: MG.10 16 PLIP interactions: 15 interactions with chain I, 1 interactions with chain J Hydrogen bonds: I:K.31, I:K.31, I:V.34, I:V.34, I:E.61, I:R.63, I:T.64, I:G.65, I:K.66, I:T.67, I:T.67, I:V.68, I:T.173, I:D.245 Salt bridges: I:K.66, J:R.189 ATP.11: 21 residues within 4Å: Chain J: K.31, S.32, I.33, V.34, V.39, E.61, S.62, R.63, T.64, G.65, K.66, T.67, V.68, T.173, W.211, I.241, G.242, D.245 Chain K: Q.185, R.189 Ligands: MG.12 17 PLIP interactions: 16 interactions with chain J, 1 interactions with chain K Hydrogen bonds: J:K.31, J:V.34, J:V.34, J:E.61, J:R.63, J:R.63, J:T.64, J:G.65, J:K.66, J:T.67, J:T.67, J:T.67, J:V.68, J:T.173, J:D.245 Salt bridges: J:K.66, K:R.189 ATP.13: 23 residues within 4Å: Chain K: K.31, S.32, I.33, V.34, V.39, E.61, 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 L: R.158, Q.185, R.189 Ligands: MG.14 19 PLIP interactions: 16 interactions with chain K, 3 interactions with chain L Hydrogen bonds: K:K.31, K:V.34, K:V.34, K:E.61, K:R.63, K:T.64, K:G.65, K:K.66, K:T.67, K:T.67, K:V.68, K:E.145, K:G.242, K:D.245, L:R.158, L:Q.185, L:R.189 Salt bridges: K:K.66, K:K.66 ATP.15: 21 residues within 4Å: Chain L: K.31, S.32, I.33, V.34, V.39, E.61, S.62, R.63, T.64, G.65, K.66, T.67, V.68, T.173, W.211, I.241, G.242, D.245 Chain M: Q.185, R.189 Ligands: MG.16 17 PLIP interactions: 16 interactions with chain L, 1 interactions with chain M Hydrogen bonds: L:K.31, L:V.34, L:V.34, L:E.61, L:R.63, L:R.63, L:T.64, L:G.65, L:K.66, L:T.67, L:T.67, L:T.67, L:V.68, L:G.242, L:D.245 Salt bridges: L:K.66, M:R.189 ATP.17: 19 residues within 4Å: Chain M: K.31, S.32, I.33, V.34, E.61, 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.18 17 PLIP interactions: 17 interactions with chain M Hydrogen bonds: M:K.31, M:K.31, M:V.34, M:V.34, M:E.61, M:R.63, M:R.63, M:T.64, M:G.65, M:K.66, M:T.67, M:V.68, M:T.173, M:G.242, M:D.245 Salt bridges: M:K.66, M:K.66

9 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain E: T.67 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.67 MG.4: 2 residues within 4Å: Chain F: T.67 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.67 MG.6: 2 residues within 4Å: Chain G: T.67 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.67 MG.8: 2 residues within 4Å: Chain H: T.67 Ligands: ATP.7 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain I: T.67 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:T.67 MG.12: 3 residues within 4Å: Chain J: T.67 Chain K: R.189 Ligands: ATP.11 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain K: T.67, D.144 Ligands: ATP.13 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:T.67 MG.16: 2 residues within 4Å: Chain L: T.67 Ligands: ATP.15 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:T.67 MG.18: 3 residues within 4Å: Chain M: T.67, D.144 Ligands: ATP.17 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:T.67

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

Cas12k: A
TnsC: EFGHIJKLM

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
R

F
S

G
T

H
U

I
V

J
W

K
X

L
Y

M
Z

Cas12k

TnsC

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