SMTL ID : 7bnk.1

Crystal structure of ParB from Myxococcus xanthus bound to CDP and Monothiophosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: R.79, D.80, V.81 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.79, A:D.80, A:D.80

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 4 residues within 4Å: Chain A: K.110, V.113, D.114, L.141 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.110, A:D.114 PEG.6: 6 residues within 4Å: Chain B: K.30, S.33, E.34, K.37, A.68 Ligands: PEG.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.30, B:S.33, B:K.37 PEG.7: 4 residues within 4Å: Chain B: E.34, K.37, V.125 Ligands: PEG.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.37, B:K.37

2 x TS6: Monothiophosphate(Non-covalent)

TS6.3: 10 residues within 4Å: Chain A: Q.19, P.20, R.21, A.58, G.59, E.60, E.93, N.94 Ligands: CDP.4, MG.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.19, A:R.21, A:G.59, A:E.60, A:N.94 TS6.8: 10 residues within 4Å: Chain B: Q.19, P.20, R.21, A.58, G.59, E.60, E.93, N.94 Ligands: CDP.9, MG.10 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.19, B:R.21, B:G.59, B:E.60, B:R.61

2 x CDP: CYTIDINE-5'-DIPHOSPHATE(Non-covalent)

CDP.4: 24 residues within 4Å: Chain A: R.21, L.32, S.35, I.36, G.40, V.41, L.42, Q.43, G.59, E.60, R.61, R.62, E.93, N.94, R.97 Chain B: Q.43, V.92, E.93, Q.96, R.97, A.98 Ligands: TS6.3, MG.5, CDP.9 21 PLIP interactions: 15 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:L.32, B:V.92, B:Q.96 Hydrogen bonds: A:G.40, A:L.42, A:Q.43, A:G.59, A:G.59, A:R.61, A:R.62, B:Q.43, B:A.98, B:A.98 Water bridges: A:E.93, A:R.97, B:R.97 Salt bridges: A:R.21, A:R.21, A:R.61, A:R.62, A:R.97 CDP.9: 23 residues within 4Å: Chain A: V.92, E.93, Q.96, R.97, A.98 Chain B: R.21, L.32, S.35, I.36, G.40, V.41, L.42, Q.43, G.59, E.60, R.61, R.62, E.93, N.94, R.97 Ligands: CDP.4, TS6.8, MG.10 21 PLIP interactions: 15 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:L.32, A:V.92, A:Q.96 Hydrogen bonds: B:G.40, B:L.42, B:Q.43, B:Q.43, B:G.59, B:G.59, B:R.61, B:R.62, A:E.93, A:A.98, A:A.98 Water bridges: B:R.97, A:R.97 Salt bridges: B:R.21, B:R.21, B:R.61, B:R.62, B:R.97

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 6 residues within 4Å: Chain A: R.21, E.93, N.94, R.97 Ligands: TS6.3, CDP.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.93, A:E.93 MG.10: 6 residues within 4Å: Chain B: R.21, E.93, N.94, R.97 Ligands: TS6.8, CDP.9 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.93, B:E.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Osorio-Valeriano, M. et al., The CTPase activity of ParB determines the size and dynamics of prokaryotic DNA partition complexes. Mol.Cell (2021)

Release Date

2021-09-08

Peptides

ParB family protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ParB family protein