SMTL ID : 8rdu.1

Conformational Landscape of the Type V-K CRISPR-associated TransposonIntegration Assembly CAST V-K composite map

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-14-8-mer

Ligands

17 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: A.173, C.174 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain K: T.67 Ligands: ATP.4 4 PLIP interactions: 1 interactions with chain K, 3 Ligand-Water interactions Metal complexes: K:T.67, H2O.13, H2O.13, H2O.13 MG.7: 3 residues within 4Å: Chain L: T.67, E.145 Ligands: ATP.6 4 PLIP interactions: 1 interactions with chain L, 3 Ligand-Water interactions Metal complexes: L:T.67, H2O.14, H2O.14, H2O.14 MG.9: 3 residues within 4Å: Chain M: T.67, E.145 Ligands: ATP.8 4 PLIP interactions: 1 interactions with chain M, 3 Ligand-Water interactions Metal complexes: M:T.67, H2O.15, H2O.15, H2O.15 MG.11: 3 residues within 4Å: Chain N: T.67, E.145 Ligands: ATP.10 4 PLIP interactions: 1 interactions with chain N, 3 Ligand-Water interactions Metal complexes: N:T.67, H2O.17, H2O.17, H2O.17 MG.13: 4 residues within 4Å: Chain O: T.67, D.144, E.145 Ligands: ATP.12 4 PLIP interactions: 1 interactions with chain O, 3 Ligand-Water interactions Metal complexes: O:T.67, H2O.19, H2O.19, H2O.19 MG.15: 4 residues within 4Å: Chain P: T.67, D.144, E.145 Ligands: ATP.14 4 PLIP interactions: 1 interactions with chain P, 3 Ligand-Water interactions Metal complexes: P:T.67, H2O.20, H2O.21, H2O.21 MG.17: 4 residues within 4Å: Chain Q: T.67, D.144, E.145 Ligands: ATP.16 4 PLIP interactions: 1 interactions with chain Q, 3 Ligand-Water interactions Metal complexes: Q:T.67, H2O.22, H2O.22, H2O.22 MG.19: 4 residues within 4Å: Chain R: T.67, D.144, E.145 Ligands: ATP.18 4 PLIP interactions: 1 interactions with chain R, 3 Ligand-Water interactions Metal complexes: R:T.67, H2O.24, H2O.24, H2O.25 MG.21: 4 residues within 4Å: Chain S: T.67, D.144, E.145 Ligands: ATP.20 4 PLIP interactions: 1 interactions with chain S, 3 Ligand-Water interactions Metal complexes: S:T.67, H2O.26, H2O.27, H2O.27 MG.23: 2 residues within 4Å: Chain T: T.67 Ligands: ATP.22 4 PLIP interactions: 1 interactions with chain T, 3 Ligand-Water interactions Metal complexes: T:T.67, H2O.28, H2O.28, H2O.29 MG.24: 2 residues within 4Å: Chain U: T.67 Ligands: ATP.25 4 PLIP interactions: 1 interactions with chain U, 3 Ligand-Water interactions Metal complexes: U:T.67, H2O.30, H2O.31, H2O.31 MG.27: 2 residues within 4Å: Chain V: T.67 Ligands: ATP.26 4 PLIP interactions: 1 interactions with chain V, 3 Ligand-Water interactions Metal complexes: V:T.67, H2O.32, H2O.32, H2O.32 MG.29: 4 residues within 4Å: Chain W: T.67, D.144, E.145 Ligands: ATP.28 4 PLIP interactions: 1 interactions with chain W, 3 Ligand-Water interactions Metal complexes: W:T.67, H2O.33, H2O.33, H2O.33 MG.30: 3 residues within 4Å: Chain X: T.67, D.144 Ligands: ATP.31 2 PLIP interactions: 1 interactions with chain X, 1 Ligand-Water interactions Metal complexes: X:T.67, H2O.33 MG.32: 4 residues within 4Å: Chain B: G.67 Chain F: C.60 Chain Y: D.205, D.287 3 PLIP interactions: 3 interactions with chain Y Metal complexes: Y:D.205, Y:D.205, Y:D.287 MG.33: 3 residues within 4Å: Chain G: T.15 Chain Z: D.205, D.287 3 PLIP interactions: 3 interactions with chain Z Metal complexes: Z:D.205, Z:D.205, Z:D.287

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain J: C.133, C.136, C.151, C.154 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.133, J:C.136, J:C.151, J:C.154 ZN.3: 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

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

ATP.4: 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.5 19 PLIP interactions: 14 interactions with chain K, 5 interactions with chain L Hydrogen bonds: K:K.31, 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:V.68, K:D.245, L:Q.185, L:Q.185 Salt bridges: K:R.63, K:K.66, K:K.66, L:R.189 Water bridges: L:R.189, L:R.189 ATP.6: 21 residues within 4Å: Chain L: 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 M: Q.185, R.189 Ligands: MG.7 24 PLIP interactions: 18 interactions with chain L, 6 interactions with chain M Hydrogen bonds: L:K.31, L:V.34, L:V.34, L:R.63, L:R.63, L:T.64, L:G.65, L:K.66, L:T.67, L:V.68, L:D.245, M:Q.185, M:Q.185 Water bridges: L:S.32, L:T.67, L:A.69, L:T.173, M:E.162, M:R.189, M:R.189 Salt bridges: L:R.63, L:K.66, L:K.66, M:R.189 ATP.8: 20 residues within 4Å: Chain M: 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 N: Q.185, R.189 Ligands: MG.9 20 PLIP interactions: 15 interactions with chain M, 5 interactions with chain N Hydrogen bonds: 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 Salt bridges: M:R.63, M:K.66, M:K.66, N:R.189 Water bridges: N:R.189, N:R.189 ATP.10: 23 residues within 4Å: Chain N: 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 O: E.162, Q.185, R.189 Ligands: MG.11 25 PLIP interactions: 19 interactions with chain N, 6 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:V.68, N:D.245, O:Q.185 Water bridges: N:K.31, N:K.66, N:T.67, N:D.144, N:E.145, N:R.249, O:E.162, O:E.162, O:R.189, O:R.189 Salt bridges: N:R.63, N:K.66, N:K.66, O:R.189 ATP.12: 22 residues within 4Å: Chain O: 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 P: Q.185, R.189 Ligands: MG.13 24 PLIP interactions: 6 interactions with chain P, 18 interactions with chain O Hydrogen bonds: P:Q.185, P:Q.185, O:K.31, O:V.34, O:V.34, 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:E.145, O:D.245 Water bridges: P:E.162, P:R.189, P:R.189, O:T.67, O:A.69 Salt bridges: P:R.189, O:R.63, O:K.66, O:K.66 ATP.14: 21 residues within 4Å: Chain P: 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 Q: Q.185, R.189 Ligands: MG.15 23 PLIP interactions: 18 interactions with chain P, 5 interactions with chain Q Hydrogen bonds: P:K.31, P:V.34, P:V.34, P:R.63, P:R.63, P:T.64, P:G.65, P:K.66, P:T.67, P:T.67, P:V.68, P:D.245, Q:Q.185, Q:Q.185 Water bridges: P:K.31, P:T.67, P:A.69, Q:R.189, Q:R.189 Salt bridges: P:R.63, P:K.66, P:K.66, Q:R.189 ATP.16: 21 residues within 4Å: Chain Q: 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 R: Q.185, R.189 Ligands: MG.17 28 PLIP interactions: 7 interactions with chain R, 21 interactions with chain Q Hydrogen bonds: R:Q.185, R:Q.185, Q:K.31, Q:V.34, Q:V.34, Q:R.63, Q:R.63, Q:T.64, Q:G.65, Q:K.66, Q:T.67, Q:T.67, Q:V.68, Q:D.245 Water bridges: R:E.162, R:E.162, R:R.189, R:R.189, Q:S.32, Q:K.66, Q:T.67, Q:A.69, Q:D.144, Q:T.173 Salt bridges: R:R.189, Q:R.63, Q:K.66, Q:K.66 ATP.18: 23 residues within 4Å: Chain R: 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 S: Q.185, R.189 Ligands: MG.19 26 PLIP interactions: 20 interactions with chain R, 6 interactions with chain S Hydrogen bonds: R:K.31, R:K.31, R:V.34, R:V.34, R:R.63, R:R.63, R:T.64, R:G.65, R:K.66, R:T.67, R:V.68, R:D.245, S:Q.185, S:Q.185 Water bridges: R:S.32, R:K.66, R:T.67, R:A.69, R:T.173, S:E.162, S:R.189, S:R.189 Salt bridges: R:R.63, R:K.66, R:K.66, S:R.189 ATP.20: 21 residues within 4Å: Chain S: 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 T: Q.185, R.189 Ligands: MG.21 23 PLIP interactions: 18 interactions with chain S, 5 interactions with chain T Hydrogen bonds: S:V.34, S:V.34, S:R.63, S:R.63, S:T.64, S:G.65, S:K.66, S:T.67, S:T.67, S:V.68, S:D.245, T:Q.185, T:Q.185 Water bridges: S:A.69, S:E.145, S:E.145, S:E.145, T:R.189, T:R.189 Salt bridges: S:K.31, S:K.66, S:K.66, T:R.189 ATP.22: 22 residues within 4Å: Chain T: 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 U: Q.185, R.189 Ligands: MG.23 24 PLIP interactions: 17 interactions with chain T, 7 interactions with chain U Hydrogen bonds: T:K.31, T:K.31, T:V.34, T:V.34, T:R.63, T:T.64, T:G.65, T:K.66, T:T.67, T:T.67, T:V.68, T:E.145, T:D.245, U:Q.185, U:Q.185 Water bridges: T:T.173, U:E.162, U:E.162, U:R.189, U:R.189 Salt bridges: T:R.63, T:K.66, T:K.66, U:R.189 ATP.25: 22 residues within 4Å: Chain U: 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 V: Q.185, R.189 Ligands: MG.24 24 PLIP interactions: 19 interactions with chain U, 5 interactions with chain V Hydrogen bonds: U:K.31, U:K.31, U:V.34, U:V.34, U:R.63, U:R.63, U:T.64, U:G.65, U:K.66, U:T.67, U:V.68, U:E.145, U:D.245, V:Q.185, V:Q.185 Water bridges: U:K.66, U:T.67, U:T.173, V:R.189, V:R.189 Salt bridges: U:R.63, U:K.66, U:K.66, V:R.189 ATP.26: 22 residues within 4Å: Chain V: 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 W: Q.185, R.189 Ligands: MG.27 22 PLIP interactions: 17 interactions with chain V, 5 interactions with chain W Hydrogen bonds: V:K.31, V:V.34, V:V.34, V:R.63, V:T.64, V:G.65, V:K.66, V:T.67, V:T.67, V:V.68, V:D.245, W:Q.185, W:Q.185 Water bridges: V:K.66, W:R.189, W:R.189 Salt bridges: V:R.63, V:R.63, V:R.63, V:K.66, V:K.66, W:R.189 ATP.28: 19 residues within 4Å: Chain W: 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 X: R.189 Ligands: MG.29 22 PLIP interactions: 19 interactions with chain W, 3 interactions with chain X Hydrogen bonds: W:V.34, W:V.34, W:S.62, W:R.63, W:R.63, W:T.64, W:G.65, W:K.66, W:T.67, W:T.67, W:V.68, W:D.245 Water bridges: W:T.67, W:D.144, X:R.189, X:R.189 Salt bridges: W:R.63, W:R.63, W:K.66, W:K.66, X:R.189 pi-Stacking: W:W.211 ATP.31: 17 residues within 4Å: Chain X: 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.30 16 PLIP interactions: 16 interactions with chain X Hydrogen bonds: X:V.34, X:V.34, X:R.63, X:T.64, X:G.65, X:K.66, X:T.67, X:T.67, X:T.67, X:V.68, X:E.145, X:D.245 Water bridges: X:T.67, X:D.144 Salt bridges: X:K.66, X: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

ShCas12k: H
Small ribosomal subunit protein uS15: I
TniQ: J
ShTnsC: KLMNOPQRSTUVWX
TnsB: YZ012345

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

H
A

I
B

J
C

K
D

L
E

M
F

N
G

O
H

P
I

Q
J

R
K

S
L

T
M

U
N

V
O

W
P

X
Q

Y
R

Z
S

0
T

1
U

2
r

3
s

4
t

5
u

ShCas12k

Small ribosomal subunit protein uS15

TniQ

ShTnsC

TnsB

Related Entries With Identical Sequence