SMTL ID : 1z5b.1

Topoisomerase VI-B, ADP AlF4- bound dimer form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: E.37, N.41, K.97 Ligands: ALF.2, ADP.4 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain B: N.41, K.97 Ligands: ALF.6, ADP.8 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain B: R.101, T.417 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:R.101, B:T.417, H2O.7, H2O.8

2 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.2: 11 residues within 4Å: Chain A: E.37, G.105, M.106, Y.107, G.108, L.109, G.110, V.111, K.426 Ligands: MG.1, ADP.4 No protein-ligand interaction detected (PLIP) ALF.6: 10 residues within 4Å: Chain B: E.37, G.105, M.106, Y.107, G.108, L.109, G.110, K.426 Ligands: MG.5, ADP.8 No protein-ligand interaction detected (PLIP)

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

SO4.3: 5 residues within 4Å: Chain A: G.265, D.266, T.267, T.268, R.306 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.265, A:T.267, A:T.268, A:T.268, A:T.268 Water bridges: A:R.306, A:R.306 Salt bridges: A:R.306

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

ADP.4: 24 residues within 4Å: Chain A: N.41, S.42, A.45, D.75, G.79, I.80, A.88, F.89, Y.94, S.95, S.96, K.97, G.105, M.106, Y.107, G.108, L.109, G.110, V.111, K.112, T.169 Chain B: F.6 Ligands: MG.1, ALF.2 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:N.41, A:D.75, A:S.95, A:S.96, A:S.96, A:M.106, A:Y.107, A:G.108, A:L.109, A:L.109, A:V.111, A:K.112, A:T.169 Water bridges: A:S.42, A:D.75, A:S.96, A:K.97, A:K.97, A:G.110 Salt bridges: A:K.97, A:K.97, A:K.112 pi-Cation interactions: A:K.97 ADP.8: 24 residues within 4Å: Chain A: F.6 Chain B: N.41, S.42, A.45, D.75, G.79, I.80, A.88, F.89, Y.94, S.95, S.96, K.97, G.105, M.106, Y.107, G.108, L.109, G.110, V.111, K.112, T.169 Ligands: MG.5, ALF.6 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:N.41, B:D.75, B:S.95, B:S.96, B:S.96, B:M.106, B:Y.107, B:G.108, B:L.109, B:L.109, B:V.111, B:K.112, B:T.169 Water bridges: B:S.42, B:D.75, B:S.96, B:G.110 Salt bridges: B:K.97, B:K.112

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Corbett, K.D. et al., Structural dissection of ATP turnover in the prototypical GHL ATPase TopoVI. Structure (2005)

Release Date

2005-06-14

Peptides

Type II DNA topoisomerase VI subunit B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Type II DNA topoisomerase VI subunit B

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