SMTL ID : 6fi8.2 (1 other biounit)

Crystal structure of the IS608 transposase in complex with left end 29-mer DNA hairpin and a 6-mer DNA representing the intact target site: pre-cleavage target capture complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x DA- DT- DT- DA- DC- DC: DNA 6-MER (T6')(Non-covalent)

DA-DT-DT-DA-DC-DC.1: 17 residues within 4Å: Chain A: C.28, Y.31, R.32, R.33, H.68, H.70, K.106, L.107, P.108 Chain B: Y.131 Chain C: A.1, A.2, A.3, G.4, C.5, C.6 Ligands: CA.11 20 PLIP interactions: 4 interactions with chain B, 16 interactions with chain A Hydrogen bonds: B:S.13, B:H.15, A:Y.31, A:Y.31, A:R.32, A:S.93, A:L.110, A:W.111, A:N.113, A:S.114 Water bridges: B:H.15, A:N.113, A:S.114, A:F.116, A:F.116 Salt bridges: B:H.15, A:K.30, A:K.30, A:K.89, A:R.97 DA-DT-DT-DA-DC-DC.2: 21 residues within 4Å: Chain A: Q.130, Y.131, I.132, E.133 Chain B: V.26, C.28, Y.31, R.32, R.33, Q.63, D.65, H.68, H.70, K.106, P.108 Chain D: A.1, A.2, A.3, G.4, C.5, C.6 Protein-ligand interaction information (PLIP) not available

9 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.3: 1 residues within 4Å: Chain A: E.61 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.61, A:E.61, H2O.1, H2O.3 CA.4: 3 residues within 4Å: Chain A: K.129, I.132 Chain B: E.61 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:K.129, A:I.132, B:E.61, B:E.61 CA.5: 2 residues within 4Å: Chain B: Q.130, E.133 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.133, H2O.3 CA.6: 2 residues within 4Å: Chain C: G.23, G.24 No protein-ligand interaction detected (PLIP) CA.7: 2 residues within 4Å: Chain C: T.28, A.29 No protein-ligand interaction detected (PLIP) CA.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.9: 1 residues within 4Å: Chain D: G.24 No protein-ligand interaction detected (PLIP) CA.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.11: 5 residues within 4Å: Chain A: D.65, H.68, H.70 Ligands: DA-DT-DT-DA-DC-DC.1, DA-DT-DT-DA-DC-DC.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.68, A:H.70, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morero, N.R. et al., Targeting IS608 transposon integration to highly specific sequences by structure-based transposon engineering. Nucleic Acids Res. (2018)

Release Date

2018-03-28

Peptides

Putative transposase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

Putative transposase

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