SMTL ID : 7mcs.1

Cryo-electron microscopy structure of TnsC(1-503)A225V bound to DNA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-heptamer

Ligands

6 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 18 residues within 4Å: Chain A: R.283, R.284 Chain B: P.66, Y.69, F.70, Q.71, G.139, S.140, G.141, K.142, T.143, T.144, D.232, E.233, F.311, M.344, V.348 Ligands: MG.2 15 PLIP interactions: 4 interactions with chain A, 11 interactions with chain B Hydrogen bonds: A:R.283, A:R.283, A:R.284, B:P.66, B:Q.71, B:Q.71, B:G.139, B:S.140, B:G.141, B:K.142, B:K.142, B:T.143, B:T.143, B:E.233 Salt bridges: A:R.283 ANP.3: 17 residues within 4Å: Chain B: R.283, R.284 Chain C: P.66, Y.69, F.70, Q.71, S.138, G.139, S.140, G.141, K.142, T.143, T.144, F.311, M.344, D.345 Ligands: MG.4 16 PLIP interactions: 13 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:P.66, C:Q.71, C:Q.71, C:S.138, C:G.139, C:S.140, C:G.141, C:K.142, C:K.142, C:T.143, C:T.143, C:T.144, C:E.233, B:R.283, B:R.284 Salt bridges: B:R.283 ANP.5: 17 residues within 4Å: Chain C: R.283, R.284 Chain D: P.66, Y.69, F.70, Q.71, S.138, G.139, S.140, G.141, K.142, T.143, T.144, E.233, M.344, D.345 Ligands: MG.6 14 PLIP interactions: 2 interactions with chain C, 12 interactions with chain D Hydrogen bonds: C:R.283, C:R.284, D:P.66, D:Q.71, D:Q.71, D:G.139, D:S.140, D:G.141, D:K.142, D:K.142, D:T.143, D:T.144, D:T.144, D:D.345 ANP.7: 17 residues within 4Å: Chain D: R.280, R.283, R.284 Chain E: P.66, Y.69, F.70, Q.71, S.138, G.139, G.141, K.142, T.143, T.144, F.311, M.344, D.345 Ligands: MG.8 12 PLIP interactions: 3 interactions with chain D, 9 interactions with chain E Hydrogen bonds: D:R.280, D:R.284, E:Q.71, E:Q.71, E:S.138, E:G.139, E:G.141, E:K.142, E:T.143, E:T.144, E:D.345 Salt bridges: D:R.283 ANP.9: 20 residues within 4Å: Chain E: R.280, R.283, R.284 Chain F: P.66, Y.69, Q.71, C.137, S.138, G.139, S.140, G.141, K.142, T.143, T.144, E.233, T.268, F.311, M.344, D.345 Ligands: MG.10 12 PLIP interactions: 10 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:P.66, F:Q.71, F:Q.71, F:G.139, F:G.141, F:K.142, F:K.142, F:T.143, F:T.144, F:D.345, E:R.283, E:R.284 ANP.11: 17 residues within 4Å: Chain F: R.283, R.284 Chain G: P.66, Y.69, F.70, Q.71, G.139, S.140, G.141, K.142, T.143, T.144, T.268, F.311, M.344, D.345 Ligands: MG.12 12 PLIP interactions: 10 interactions with chain G, 2 interactions with chain F Hydrogen bonds: G:P.66, G:Q.71, G:Q.71, G:G.139, G:S.140, G:G.141, G:K.142, G:T.143, G:T.144, G:D.345, F:R.283, F:R.284

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain B: T.143, D.232 Ligands: ANP.1 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.143 MG.4: 2 residues within 4Å: Chain C: T.143 Ligands: ANP.3 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.143 MG.6: 3 residues within 4Å: Chain D: T.143, D.232 Ligands: ANP.5 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.143 MG.8: 3 residues within 4Å: Chain E: T.143, D.232 Ligands: ANP.7 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.143 MG.10: 4 residues within 4Å: Chain F: T.143, D.232, E.233 Ligands: ANP.9 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.143 MG.12: 3 residues within 4Å: Chain F: R.284 Chain G: T.143 Ligands: ANP.11 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.143

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shen, Y. et al., Structural basis for DNA targeting by the Tn7 transposon. Nat.Struct.Mol.Biol. (2022)

Release Date

2022-02-23

Peptides

Transposon Tn7 transposition protein TnsC: ABCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

Transposon Tn7 transposition protein TnsC

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