SMTL ID : 5j5q.2 (1 other biounit)

AMP-PNP-stabilized ATPase domain of topoisomerase IV from Streptococcus pneumoniae, complex type II

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.83 Å

Oligo State

homo-dimer

Ligands

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

ANP.1: 25 residues within 4Å: Chain A: E.48, N.52, E.56, D.79, G.83, M.84, I.99, A.105, G.106, G.107, K.108, Y.114, G.119, L.120, H.121, G.122, V.123, G.124, S.125, S.126, T.173, K.345 Chain B: Y.12, I.17 Ligands: MG.2 22 PLIP interactions: 20 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.48, A:N.52, A:D.79, A:G.107, A:K.108, A:K.108, A:K.108, A:Y.114, A:L.120, A:H.121, A:G.122, A:V.123, A:G.124, A:S.125, A:S.126, A:T.173, A:K.345, A:K.345, B:Y.12, B:Y.12 Salt bridges: A:K.108 pi-Cation interactions: A:K.108 ANP.3: 24 residues within 4Å: Chain A: Y.12 Chain B: E.48, N.52, A.53, E.56, D.79, G.83, M.84, I.99, A.105, G.106, G.107, K.108, Y.114, G.119, L.120, H.121, G.122, V.123, G.124, S.125, S.126, T.173 Ligands: MG.4 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.52, B:E.56, B:D.79, B:G.107, B:Y.114, B:L.120, B:H.121, B:G.122, B:V.123, B:V.123, B:G.124, B:S.125, B:S.126, A:Y.12, A:Y.12 pi-Cation interactions: B:K.108

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: E.48, N.52, K.108 Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain B: E.48, N.52 Ligands: ANP.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Laponogov, I. et al., Trapping of the transport-segment DNA by the ATPase domains of a type II topoisomerase. Nat Commun (2018)

Release Date

2017-07-26

Peptides

DNA topoisomerase 4 subunit B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

DNA topoisomerase 4 subunit B

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