SMTL ID : 8rku.1

Conformational Landscape of the Type V-K CRISPR-associated TransposonIntegration Assembly CAST V-K TnsC domain local-refinement map

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-14-mer

Ligands

14 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain C: T.67 Ligands: ATP.2 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.67, H2O.1, H2O.1, H2O.1 MG.4: 3 residues within 4Å: Chain D: T.67, E.145 Ligands: ATP.3 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:T.67, H2O.1, H2O.2, H2O.2 MG.6: 3 residues within 4Å: Chain E: T.67, E.145 Ligands: ATP.5 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:T.67, H2O.2, H2O.3, H2O.3 MG.8: 3 residues within 4Å: Chain F: T.67, E.145 Ligands: ATP.7 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:T.67, H2O.5, H2O.5, H2O.5 MG.10: 4 residues within 4Å: Chain G: T.67, D.144, E.145 Ligands: ATP.9 4 PLIP interactions: 1 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:T.67, H2O.6, H2O.6, H2O.6 MG.12: 4 residues within 4Å: Chain H: T.67, D.144, E.145 Ligands: ATP.11 4 PLIP interactions: 1 interactions with chain H, 3 Ligand-Water interactions Metal complexes: H:T.67, H2O.8, H2O.8, H2O.8 MG.14: 4 residues within 4Å: Chain I: T.67, D.144, E.145 Ligands: ATP.13 4 PLIP interactions: 1 interactions with chain I, 3 Ligand-Water interactions Metal complexes: I:T.67, H2O.10, H2O.10, H2O.10 MG.16: 4 residues within 4Å: Chain J: T.67, D.144, E.145 Ligands: ATP.15 4 PLIP interactions: 1 interactions with chain J, 3 Ligand-Water interactions Metal complexes: J:T.67, H2O.12, H2O.12, H2O.12 MG.18: 4 residues within 4Å: Chain K: T.67, D.144, E.145 Ligands: ATP.17 4 PLIP interactions: 1 interactions with chain K, 3 Ligand-Water interactions Metal complexes: K:T.67, H2O.14, H2O.14, H2O.14 MG.20: 2 residues within 4Å: Chain L: T.67 Ligands: ATP.19 4 PLIP interactions: 1 interactions with chain L, 3 Ligand-Water interactions Metal complexes: L:T.67, H2O.16, H2O.16, H2O.17 MG.22: 2 residues within 4Å: Chain M: T.67 Ligands: ATP.21 4 PLIP interactions: 1 interactions with chain M, 3 Ligand-Water interactions Metal complexes: M:T.67, H2O.18, H2O.18, H2O.18 MG.24: 2 residues within 4Å: Chain N: T.67 Ligands: ATP.23 4 PLIP interactions: 1 interactions with chain N, 3 Ligand-Water interactions Metal complexes: N:T.67, H2O.19, H2O.19, H2O.20 MG.26: 4 residues within 4Å: Chain O: T.67, D.144, E.145 Ligands: ATP.25 4 PLIP interactions: 1 interactions with chain O, 3 Ligand-Water interactions Metal complexes: O:T.67, H2O.21, H2O.21, H2O.21 MG.27: 3 residues within 4Å: Chain P: T.67, D.144 Ligands: ATP.28 2 PLIP interactions: 1 interactions with chain P, 1 Ligand-Water interactions Metal complexes: P:T.67, H2O.21

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

ATP.2: 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: Q.185, R.189 Ligands: MG.1 19 PLIP interactions: 14 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:K.31, C:V.34, C:V.34, C:R.63, C:R.63, C:T.64, C:G.65, C:K.66, C:T.67, C:V.68, C:D.245, D:Q.185, D:Q.185 Salt bridges: C:R.63, C:K.66, C:K.66, D:R.189 Water bridges: D:R.189, D:R.189 ATP.3: 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: Q.185, R.189 Ligands: MG.4 24 PLIP interactions: 18 interactions with chain D, 6 interactions with chain E Hydrogen bonds: D:K.31, D:V.34, D:V.34, D:R.63, D:R.63, D:T.64, D:G.65, D:K.66, D:T.67, D:V.68, D:D.245, E:Q.185, E:Q.185 Water bridges: D:S.32, D:T.67, D:A.69, D:T.173, E:E.162, E:R.189, E:R.189 Salt bridges: D:R.63, D:K.66, D:K.66, E:R.189 ATP.5: 20 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, E.145, T.173, W.211, I.241, G.242, D.245 Chain F: Q.185, R.189 Ligands: MG.6 20 PLIP interactions: 15 interactions with chain E, 5 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:V.68, E:E.145, E:D.245, F:Q.185, F:Q.185 Salt bridges: E:R.63, E:K.66, E:K.66, F:R.189 Water bridges: F:R.189, F:R.189 ATP.7: 23 residues within 4Å: Chain F: 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 G: E.162, Q.185, R.189 Ligands: MG.8 25 PLIP interactions: 19 interactions with chain F, 6 interactions with chain G Hydrogen bonds: 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:V.68, F:D.245, G:Q.185 Water bridges: F:K.31, F:K.66, F:T.67, F:D.144, F:E.145, F:R.249, G:E.162, G:E.162, G:R.189, G:R.189 Salt bridges: F:R.63, F:K.66, F:K.66, G:R.189 ATP.9: 22 residues within 4Å: Chain G: K.31, S.32, I.33, V.34, L.36, 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 H: Q.185, R.189 Ligands: MG.10 24 PLIP interactions: 6 interactions with chain H, 18 interactions with chain G Hydrogen bonds: H:Q.185, H:Q.185, G:K.31, G:V.34, G:V.34, G:R.63, 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:D.245 Water bridges: H:E.162, H:R.189, H:R.189, G:T.67, G:A.69 Salt bridges: H:R.189, G:R.63, G:K.66, G:K.66 ATP.11: 21 residues within 4Å: Chain H: 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 I: Q.185, R.189 Ligands: MG.12 23 PLIP interactions: 18 interactions with chain H, 5 interactions with chain I Hydrogen bonds: H:K.31, H:V.34, H:V.34, H:R.63, H:R.63, H:T.64, H:G.65, H:K.66, H:T.67, H:T.67, H:V.68, H:D.245, I:Q.185, I:Q.185 Water bridges: H:K.31, H:T.67, H:A.69, I:R.189, I:R.189 Salt bridges: H:R.63, H:K.66, H:K.66, I:R.189 ATP.13: 21 residues within 4Å: Chain I: 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 J: Q.185, R.189 Ligands: MG.14 28 PLIP interactions: 21 interactions with chain I, 7 interactions with chain J Hydrogen bonds: I:K.31, I:V.34, I:V.34, I:R.63, I:R.63, I:T.64, I:G.65, I:K.66, I:T.67, I:T.67, I:V.68, I:D.245, J:Q.185, J:Q.185 Water bridges: I:S.32, I:K.66, I:T.67, I:A.69, I:D.144, I:T.173, J:E.162, J:E.162, J:R.189, J:R.189 Salt bridges: I:R.63, I:K.66, I:K.66, J:R.189 ATP.15: 23 residues within 4Å: Chain J: K.31, S.32, I.33, V.34, L.36, 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 K: Q.185, R.189 Ligands: MG.16 27 PLIP interactions: 21 interactions with chain J, 6 interactions with chain K Hydrogen bonds: J:K.31, J:K.31, J:V.34, J:V.34, J:R.63, J:R.63, J:T.64, J:G.65, J:K.66, J:T.67, J:T.67, J:V.68, J:D.245, K:Q.185, K:Q.185 Water bridges: J:S.32, J:K.66, J:T.67, J:A.69, J:T.173, K:E.162, K:R.189, K:R.189 Salt bridges: J:R.63, J:K.66, J:K.66, K:R.189 ATP.17: 21 residues within 4Å: Chain K: 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 L: Q.185, R.189 Ligands: MG.18 23 PLIP interactions: 18 interactions with chain K, 5 interactions with chain L Hydrogen bonds: K:V.34, K:V.34, K:R.63, K:R.63, K:T.64, K:G.65, K:K.66, K:T.67, K:T.67, K:V.68, K:D.245, L:Q.185, L:Q.185 Water bridges: K:A.69, K:E.145, K:E.145, K:E.145, L:R.189, L:R.189 Salt bridges: K:K.31, K:K.66, K:K.66, L:R.189 ATP.19: 22 residues within 4Å: Chain L: K.31, S.32, I.33, 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 M: Q.185, R.189 Ligands: MG.20 24 PLIP interactions: 17 interactions with chain L, 7 interactions with chain M Hydrogen bonds: L:K.31, L:K.31, L:V.34, L:V.34, L:R.63, L:T.64, L:G.65, L:K.66, L:T.67, L:T.67, L:V.68, L:E.145, L:D.245, M:Q.185, M:Q.185 Water bridges: L:T.173, M:E.162, M:E.162, M:R.189, M:R.189 Salt bridges: L:R.63, L:K.66, L:K.66, M:R.189 ATP.21: 22 residues within 4Å: Chain M: K.31, S.32, I.33, 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 N: Q.185, R.189 Ligands: MG.22 24 PLIP interactions: 19 interactions with chain M, 5 interactions with chain N Hydrogen bonds: M:K.31, M:K.31, M:V.34, M:V.34, M:R.63, M:R.63, M:T.64, M:G.65, M:K.66, M:T.67, M:V.68, M:E.145, M:D.245, N:Q.185, N:Q.185 Water bridges: M:K.66, M:T.67, M:T.173, N:R.189, N:R.189 Salt bridges: M:R.63, M:K.66, M:K.66, N:R.189 ATP.23: 22 residues within 4Å: Chain N: K.31, S.32, I.33, V.34, L.36, 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 O: Q.185, R.189 Ligands: MG.24 22 PLIP interactions: 17 interactions with chain N, 5 interactions with chain O Hydrogen bonds: N:K.31, N:V.34, N:V.34, N:R.63, N:T.64, N:G.65, N:K.66, N:T.67, N:T.67, N:V.68, N:D.245, O:Q.185, O:Q.185 Water bridges: N:K.66, O:R.189, O:R.189 Salt bridges: N:R.63, N:R.63, N:R.63, N:K.66, N:K.66, O:R.189 ATP.25: 19 residues within 4Å: Chain O: 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 Chain P: R.189 Ligands: MG.26 22 PLIP interactions: 19 interactions with chain O, 3 interactions with chain P Hydrogen bonds: O:V.34, O:V.34, O:S.62, O:R.63, O:R.63, O:T.64, O:G.65, O:K.66, O:T.67, O:T.67, O:V.68, O:D.245 Water bridges: O:T.67, O:D.144, P:R.189, P:R.189 Salt bridges: O:R.63, O:R.63, O:K.66, O:K.66, P:R.189 pi-Stacking: O:W.211 ATP.28: 17 residues within 4Å: Chain P: S.32, I.33, V.34, E.61, S.62, R.63, T.64, G.65, K.66, T.67, V.68, E.145, W.211, I.241, G.242, D.245 Ligands: MG.27 15 PLIP interactions: 15 interactions with chain P Hydrogen bonds: P:V.34, P:V.34, P:R.63, P:T.64, P:G.65, P:K.66, P:T.67, P:T.67, P:V.68, P:E.145, P:D.245 Water bridges: P:T.67, P:D.144 Salt bridges: P:K.66, P:K.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tenjo-Castano, F. et al., Conformational landscape of the type V-K CRISPR-associated transposon integration assembly. Mol.Cell (2024)

Release Date

2024-06-19

Peptides

ShTnsC: CDEFGHIJKLMNOP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

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

ShTnsC

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