SMTL ID : 5tgx.1 (2 other biounits)

Restriction/modification system-Type II R-SwaI complexed with partially cleaved DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.76, D.93, F.94 Chain E: A.15 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.76, A:D.93, A:F.94, H2O.2, H2O.7 CA.6: 4 residues within 4Å: Chain B: D.76, D.93, F.94 Chain F: A.15 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.76, B:D.93, B:F.94, H2O.3, H2O.3 CA.8: 4 residues within 4Å: Chain C: D.76, D.93, F.94 Chain G: A.15 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.76, C:D.93, C:F.94, H2O.4, H2O.4 CA.9: 5 residues within 4Å: Chain D: D.76, D.93, F.94, K.95 Chain H: A.15 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.76, D:D.93, D:F.94, H2O.5, H2O.6

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 5 residues within 4Å: Chain A: G.65, A.66, P.67 Chain D: Y.61, D.62 No protein-ligand interaction detected (PLIP) EDO.3: 5 residues within 4Å: Chain A: E.159, S.160, K.192 Chain F: G.9, C.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.192 EDO.4: 4 residues within 4Å: Chain A: S.160, R.162 Chain F: G.9, C.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.162 Water bridges: A:S.160 EDO.5: 3 residues within 4Å: Chain A: E.69 Chain D: K.82, E.87 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.82 EDO.10: 4 residues within 4Å: Chain D: E.159, S.160, K.192 Chain G: C.10 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.159 Water bridges: D:K.192, D:E.195 EDO.11: 5 residues within 4Å: Chain A: K.72 Chain E: A.11, T.12 Chain F: G.19, C.20 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.72, A:K.72

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 2 residues within 4Å: Chain B: F.141, Y.148 1 PLIP interactions: 1 interactions with chain B Water bridges: B:F.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shen, B.W. et al., DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair A:T-rich target. Nucleic Acids Res. (2017)

Release Date

2016-12-21

Peptides

R-SwaI protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

R-SwaI protein

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