SMTL ID : 4rul.1

Crystal structure of full-length E.Coli topoisomerase I in complex with ssDNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

monomer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.601, C.604, C.621, C.632, T.634 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.601, A:C.604, A:C.621, A:C.632 ZN.2: 4 residues within 4Å: Chain A: C.664, C.667, C.685, C.691 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.664, A:C.667, A:C.685, A:C.691 ZN.3: 5 residues within 4Å: Chain A: C.713, C.716, S.718, C.733, C.738 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.713, A:C.716, A:C.733, A:C.738 ZN.4: 1 residues within 4Å: Chain A: H.568 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.568

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 3 residues within 4Å: Chain A: R.171, R.175, Y.179 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.171, A:R.175 SO4.6: 3 residues within 4Å: Chain A: R.116, R.163, A.556 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.163 Salt bridges: A:R.116, A:R.163 SO4.7: 4 residues within 4Å: Chain A: G.302, E.481, V.514, R.517 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.517 Water bridges: A:G.302 Salt bridges: A:R.517 SO4.8: 4 residues within 4Å: Chain A: S.296, T.297, R.517, R.518 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.517, A:R.518

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain A: Y.85, W.123, N.165, Q.168, W.562 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tan, K. et al., Structural basis for suppression of hypernegative DNA supercoiling by E. coli topoisomerase I. Nucleic Acids Res. (2015)

Release Date

2015-11-04

Peptides

DNA topoisomerase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA topoisomerase 1