SMTL ID : 7ola.1

Structure of Primase-Helicase in SaPI5

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

4 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 19 residues within 4Å: Chain A: W.485, E.488, G.524, N.525, N.526, G.527, K.528, G.529, T.530, D.571, S.614, F.641, K.645, E.646, N.647, F.648, I.650, K.651 Chain F: R.630 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:E.488, A:N.525, A:N.526, A:G.527, A:G.527, A:K.528, A:K.528, A:K.528, A:G.529, A:T.530, A:T.530, A:S.614, A:S.614, A:N.647, F:R.630 pi-Stacking: A:F.641 ANP.2: 21 residues within 4Å: Chain A: G.627, R.630, R.631 Chain B: W.485, D.523, G.524, N.525, N.526, G.527, K.528, G.529, T.530, N.616, F.641, K.645, E.646, N.647, F.648, I.650, K.651 Ligands: MG.3 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.488, B:N.525, B:N.526, B:G.527, B:K.528, B:K.528, B:G.529, B:T.530, B:N.616, B:N.616, B:N.647, B:K.651, A:R.631 Salt bridges: B:K.651 pi-Stacking: B:F.641, B:F.641 ANP.5: 20 residues within 4Å: Chain B: D.591, G.627, R.630, R.631 Chain C: W.485, G.524, N.525, N.526, G.527, K.528, G.529, T.530, F.641, K.645, E.646, N.647, F.648, I.650, K.651 Ligands: MG.4 22 PLIP interactions: 17 interactions with chain C, 5 interactions with chain B Hydrogen bonds: C:W.485, C:N.525, C:N.526, C:G.527, C:K.528, C:K.528, C:K.528, C:G.529, C:T.530, C:E.646, C:E.646, C:N.647, C:F.648, C:K.651, B:R.630, B:R.630, B:R.631, B:R.631, B:R.631 Salt bridges: C:K.651 pi-Stacking: C:F.641, C:F.641 ANP.6: 19 residues within 4Å: Chain C: G.627, R.630, R.631 Chain D: W.485, E.488, I.489, G.524, N.526, G.527, K.528, G.529, T.530, F.641, E.646, N.647, F.648, I.650, K.651 Ligands: MG.7 22 PLIP interactions: 18 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:E.488, D:G.524, D:G.524, D:N.526, D:G.527, D:K.528, D:K.528, D:K.528, D:G.529, D:T.530, D:E.646, D:E.646, D:N.647, D:F.648, D:K.651, C:R.630, C:R.631, C:R.631 Salt bridges: D:K.651, C:R.630 pi-Stacking: D:F.641, D:F.641

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.591, R.631 Ligands: ANP.2 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain B: D.591, R.631 Ligands: ANP.5 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain C: R.631 Ligands: ANP.6 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qiao, C. et al., Staphylococcal self-loading helicases couple the staircase mechanism with inter domain high flexibility. Nucleic Acids Res. (2022)

Release Date

2022-07-13

Peptides

DNA primase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

DNA primase

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