SMTL ID : 6sdk.1 (1 other biounit)

Crystal structure of bacterial ParB dimer bound to CDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

homo-dimer

Ligands

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

CDP.1: 23 residues within 4Å: Chain A: R.20, L.31, S.34, V.35, H.38, G.39, I.40, L.41, Q.42, G.58, E.59, R.60, R.61, E.92, N.93, R.96 Chain B: L.91, E.92, Q.95, R.96, E.97 Ligands: CA.2, CA.3 25 PLIP interactions: 19 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:L.31, B:Q.95 Hydrogen bonds: A:G.39, A:L.41, A:Q.42, A:G.58, A:G.58, A:E.59, A:R.60, A:R.61, B:E.92, B:E.97, B:E.97 Water bridges: A:R.20, A:R.61, A:E.92, A:N.93, A:R.96, A:R.96, B:E.92, B:E.92 Salt bridges: A:R.20, A:R.60, A:R.61, A:R.96 CDP.4: 22 residues within 4Å: Chain A: L.91, E.92, Q.95, R.96, E.97 Chain B: R.20, L.31, S.34, V.35, H.38, G.39, I.40, L.41, Q.42, G.58, E.59, R.60, R.61, E.92, N.93, R.96 Ligands: CA.5 25 PLIP interactions: 19 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:L.31, A:Q.95 Hydrogen bonds: B:G.39, B:L.41, B:Q.42, B:Q.42, B:G.58, B:G.58, B:E.59, B:R.60, B:R.61, A:E.92, A:E.92, A:E.97, A:E.97 Water bridges: B:R.20, B:R.61, B:N.93, B:R.96, B:R.96, A:R.96 Salt bridges: B:R.20, B:R.60, B:R.61, B:R.96

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: R.20, R.61, E.92, N.93, R.96 Ligands: CDP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.92, H2O.1, H2O.2, H2O.4 CA.3: 7 residues within 4Å: Chain A: N.15, Q.18, I.55, A.57, G.58, E.59 Ligands: CDP.1 No protein-ligand interaction detected (PLIP) CA.5: 6 residues within 4Å: Chain B: R.20, R.61, E.92, N.93, R.96 Ligands: CDP.4 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.92, H2O.6, H2O.6, H2O.8 CA.6: 6 residues within 4Å: Chain B: N.15, Q.18, I.55, A.57, G.58, E.59 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Soh, Y.M. et al., Self-organization ofparScentromeres by the ParB CTP hydrolase. Science (2019)

Release Date

2019-10-23

Peptides

Stage 0 sporulation protein J: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Stage 0 sporulation protein J

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