SMTL ID : 7om0.1

Structure of Primase-Helicase in SaPI5

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

ANP.1: 21 residues within 4Å: Chain A: W.485, E.488, G.524, N.525, N.526, G.527, K.528, G.529, T.530, D.570, N.616, F.641, K.645, E.646, N.647, F.648, I.650, K.651 Chain B: D.591, R.630, R.631 18 PLIP interactions: 13 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:W.485, A:N.526, A:G.527, A:K.528, A:K.528, A:K.528, A:G.529, A:T.530, A:N.647, A:K.651, B:R.630, B:R.630, B:R.631, B:R.631 Salt bridges: A:K.651, B:R.630 pi-Stacking: A:F.641, A:F.641 ANP.2: 21 residues within 4Å: Chain B: W.485, E.488, G.524, N.525, N.526, G.527, K.528, G.529, T.530, D.570, N.616, F.641, K.645, E.646, N.647, F.648, I.650, K.651 Chain F: D.591, R.630, R.631 20 PLIP interactions: 15 interactions with chain B, 5 interactions with chain F Hydrogen bonds: B:W.485, B:N.526, B:G.527, B:K.528, B:K.528, B:K.528, B:G.529, B:T.530, B:D.571, B:S.614, B:N.647, B:F.648, B:K.651, F:R.630, F:R.630, F:R.631, F:R.631 pi-Stacking: B:F.641, B:F.641 Salt bridges: F:R.630 ANP.3: 21 residues within 4Å: Chain A: D.591, R.630, R.631 Chain C: W.485, E.488, G.524, N.525, N.526, G.527, K.528, G.529, T.530, D.570, N.616, F.641, K.645, E.646, N.647, F.648, I.650, K.651 18 PLIP interactions: 13 interactions with chain C, 5 interactions with chain A Hydrogen bonds: C:W.485, C:N.526, C:G.527, C:K.528, C:K.528, C:K.528, C:G.529, C:T.530, C:N.647, C:K.651, A:R.630, A:R.630, A:R.631, A:R.631 Salt bridges: C:K.651, A:R.630 pi-Stacking: C:F.641, C:F.641 ANP.4: 21 residues within 4Å: Chain D: W.485, E.488, G.524, N.525, N.526, G.527, K.528, G.529, T.530, D.570, N.616, F.641, K.645, E.646, N.647, F.648, I.650, K.651 Chain E: D.591, R.630, R.631 18 PLIP interactions: 13 interactions with chain D, 5 interactions with chain E Hydrogen bonds: D:W.485, D:N.526, D:G.527, D:K.528, D:K.528, D:K.528, D:G.529, D:T.530, D:N.647, D:K.651, E:R.630, E:R.630, E:R.631, E:R.631 Salt bridges: D:K.651, E:R.630 pi-Stacking: D:F.641, D:F.641 ANP.5: 21 residues within 4Å: Chain C: D.591, R.630, R.631 Chain E: W.485, E.488, G.524, N.525, N.526, G.527, K.528, G.529, T.530, D.570, N.616, F.641, K.645, E.646, N.647, F.648, I.650, K.651 18 PLIP interactions: 13 interactions with chain E, 5 interactions with chain C Hydrogen bonds: E:W.485, E:N.526, E:G.527, E:K.528, E:K.528, E:K.528, E:G.529, E:T.530, E:N.647, E:F.648, E:K.651, C:R.630, C:R.630, C:R.631, C:R.631 pi-Stacking: E:F.641, E:F.641 Salt bridges: C:R.630 ANP.6: 20 residues within 4Å: Chain D: D.591, R.630, R.631 Chain F: W.485, E.488, N.525, N.526, G.527, K.528, G.529, T.530, D.570, N.616, F.641, K.645, E.646, N.647, F.648, I.650, K.651 20 PLIP interactions: 15 interactions with chain F, 5 interactions with chain D Hydrogen bonds: F:W.485, F:N.525, F:N.526, F:G.527, F:K.528, F:K.528, F:K.528, F:G.529, F:T.530, F:N.616, F:N.647, F:K.651, D:R.630, D:R.630, D:R.631, D:R.631 Salt bridges: F:K.651, D:R.630 pi-Stacking: F:F.641, F:F.641

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
F

D
D

E
E

F
C

DNA primase

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