SMTL ID : 5j5p.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-dimer

Ligands

4 x DG- DC- DG- DC- DG- DC: DNA (5'-D(*GP*CP*GP*CP*GP*C)-3')(Non-covalent)

DG-DC-DG-DC-DG-DC.1: 17 residues within 4Å: Chain A: K.282 Chain B: T.289, K.292, S.293, T.296, K.297, N.300, N.315, G.318, R.322, K.347 Ligands: DG-DC-DG-DC-DG-DC.2, DG-DC-DG-DC-DG-DC.2, DG-DC-DG-DC-DG-DC.2, DG-DC-DG-DC-DG-DC.2, DG-DC-DG-DC-DG-DC.2, DG-DC-DG-DC-DG-DC.2 Protein-ligand interaction information (PLIP) not available DG-DC-DG-DC-DG-DC.2: 8 residues within 4Å: Chain B: R.354, P.355 Ligands: DG-DC-DG-DC-DG-DC.1, DG-DC-DG-DC-DG-DC.1, DG-DC-DG-DC-DG-DC.1, DG-DC-DG-DC-DG-DC.1, DG-DC-DG-DC-DG-DC.1, DG-DC-DG-DC-DG-DC.1 Protein-ligand interaction information (PLIP) not available DG-DC-DG-DC-DG-DC.3: 18 residues within 4Å: Chain A: E.288, T.289, K.292, S.293, T.296, K.297, N.300, N.315, G.318, R.322, K.347 Chain B: K.282 Ligands: DG-DC-DG-DC-DG-DC.4, DG-DC-DG-DC-DG-DC.4, DG-DC-DG-DC-DG-DC.4, DG-DC-DG-DC-DG-DC.4, DG-DC-DG-DC-DG-DC.4, DG-DC-DG-DC-DG-DC.4 Protein-ligand interaction information (PLIP) not available DG-DC-DG-DC-DG-DC.4: 8 residues within 4Å: Chain A: R.354, P.355 Ligands: DG-DC-DG-DC-DG-DC.3, DG-DC-DG-DC-DG-DC.3, DG-DC-DG-DC-DG-DC.3, DG-DC-DG-DC-DG-DC.3, DG-DC-DG-DC-DG-DC.3, DG-DC-DG-DC-DG-DC.3 Protein-ligand interaction information (PLIP) not available

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

ANP.5: 28 residues within 4Å: Chain A: 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, Q.343, K.345 Chain B: Y.12, I.17 Ligands: NA.6, MG.7 21 PLIP interactions: 20 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.52, A:D.79, A:G.107, 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:Q.343, A:K.345, B:Y.12 Water bridges: A:E.48, A:E.48, A:K.108 pi-Cation interactions: A:K.108 ANP.9: 28 residues within 4Å: Chain A: Y.12, I.17 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, Q.343, K.345 Ligands: NA.10, MG.11 23 PLIP interactions: 22 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.56, B:D.79, B:G.107, B:K.108, B:L.120, B:H.121, B:G.122, B:V.123, B:V.123, B:G.124, B:S.125, B:S.126, B:Q.343, B:K.345, B:K.345, A:Y.12 Water bridges: B:E.48, B:N.52, B:D.79, B:K.108, B:T.173, B:T.173 pi-Cation interactions: B:K.108

2 x NA: SODIUM ION(Non-functional Binders)

NA.6: 6 residues within 4Å: Chain A: I.99, I.102, A.105, G.122, S.126 Ligands: ANP.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.99, A:A.105 NA.10: 6 residues within 4Å: Chain B: I.99, I.102, A.105, G.122, S.126 Ligands: ANP.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.102

4 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 3 residues within 4Å: Chain A: N.52, K.108 Ligands: ANP.5 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain A: K.282, D.346 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain B: N.52, K.108 Ligands: ANP.9 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain B: D.346 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
A

B
B

DNA topoisomerase 4 subunit B

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