SMTL ID : 4r1f.1 (1 other biounit)

Re-refined Human DNA topoisomerase IIa (ATPase and transducer domains) in complex with ADP and SO4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.59, N.63 Ligands: ADP.2 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain B: N.63 Ligands: ADP.6 No protein-ligand interaction detected (PLIP)

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 22 residues within 4Å: Chain A: N.63, N.67, R.70, N.92, I.97, I.113, F.114, T.119, S.120, S.121, N.122, G.133, R.134, N.135, G.136, Y.137, G.138, A.139, K.140, T.187 Chain B: Y.6 Ligands: MG.1 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:N.63, A:N.92, A:N.92, A:S.120, A:S.120, A:S.121, A:S.121, A:N.122, A:R.134, A:N.135, A:G.136, A:Y.137, A:A.139, A:T.187 Water bridges: A:G.138, A:G.138 Salt bridges: A:K.140 ADP.6: 23 residues within 4Å: Chain A: Y.6 Chain B: N.63, N.67, R.70, N.92, I.97, I.113, F.114, T.119, S.120, S.121, N.122, G.133, R.134, N.135, G.136, Y.137, G.138, A.139, K.140, T.187 Ligands: MG.4, SO4.5 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:N.92, B:S.120, B:S.121, B:S.121, B:N.122, B:R.134, B:N.135, B:G.136, B:Y.137, B:A.139 Water bridges: B:E.59, B:N.63, B:N.63, B:D.66, B:N.92, B:N.92, B:G.138 Salt bridges: B:K.140

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: Y.22, K.55, E.59, N.135, Y.137, G.138, Q.348, K.350 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.55, A:N.135, A:G.138, A:K.350, A:K.350 Water bridges: A:E.59

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

SO4.5: 8 residues within 4Å: Chain B: E.59, R.134, N.135, G.136, Y.137, G.138, K.350 Ligands: ADP.6 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:R.134, B:N.135, B:N.135, B:Y.137, B:G.138 Water bridges: B:K.55, B:E.59, B:E.59 Salt bridges: B:K.55, B:K.350

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stanger, F.V. et al., Structure of the N-Terminal Gyrase B Fragment in Complex with ADPPi Reveals Rigid-Body Motion Induced by ATP Hydrolysis. Plos One (2014)

Release Date

2014-09-24

Peptides

DNA topoisomerase 2-alpha: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA topoisomerase 2-alpha

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