SMTL ID : 3m6z.1 (1 other biounit)

Crystal structure of an N-terminal 44 kDa fragment of topoisomerase V in the presence of guanidium hydrochloride

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 7 residues within 4Å: Chain A: R.108, R.131, V.133, R.144, R.293, S.322, S.324 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:R.131 Water bridges: A:R.108, A:R.144, A:R.293, A:R.293, A:R.293, A:I.323, A:I.323, A:I.323, A:S.324 Salt bridges: A:R.108, A:R.131, A:R.144, A:R.293 PO4.2: 4 residues within 4Å: Chain A: R.42, L.269, R.270, H.271 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.271, A:H.271 Salt bridges: A:R.42, A:H.271 PO4.3: 5 residues within 4Å: Chain A: R.37, K.47, K.134, R.135, Q.292 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.292 Salt bridges: A:R.37, A:K.47, A:R.135

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 6 residues within 4Å: Chain A: S.210, V.211, A.327, V.349, N.350, R.351 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:V.349 MG.5: 2 residues within 4Å: Chain A: E.266, L.269 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.266, A:L.269, H2O.105, H2O.106

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 3 residues within 4Å: Chain A: S.12, E.13, R.14 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: V.4, Y.5, K.116 Ligand excluded by PLIP

2 x GAI: GUANIDINE(Non-covalent)

GAI.8: 3 residues within 4Å: Chain A: V.133, K.134, R.293 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.133, A:K.134, A:R.293 Water bridges: A:K.134, A:K.134, A:R.293 GAI.9: 4 residues within 4Å: Chain A: V.159, D.160, V.162, P.164 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.162 Water bridges: A:D.160

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rajan, R. et al., Structures of minimal catalytic fragments of topoisomerase v reveals conformational changes relevant for DNA binding. Structure (2010)

Release Date

2010-08-04

Peptides

Topoisomerase V: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Topoisomerase V

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