SMTL ID : 8bv3.1

Bacillus subtilis DnaA domain III structure

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

homo-pentamer

Ligands

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

ANP.1: 22 residues within 4Å: Chain A: Y.12, T.16, F.17, V.18, N.23, G.49, V.50, G.51, L.52, G.53, K.54, T.55, H.56, D.112, I.181, K.185, I.209, R.210, E.213 Chain B: R.161, W.164 Ligands: MG.3 19 PLIP interactions: 16 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Y.12, A:V.18, A:V.18, A:G.51, A:L.52, A:G.53, A:K.54, A:K.54, A:K.54, A:T.55, A:H.56, A:K.185, A:R.210, A:R.210, B:R.161, B:R.161, B:W.164 Salt bridges: A:R.210 pi-Cation interactions: A:H.56 ANP.4: 22 residues within 4Å: Chain B: Y.12, T.16, F.17, V.18, N.23, G.49, V.50, G.51, L.52, G.53, K.54, T.55, H.56, D.112, I.181, K.185, I.209, R.210, E.213 Chain C: R.161, W.164 Ligands: MG.7 21 PLIP interactions: 18 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:Y.12, B:V.18, B:V.18, B:G.51, B:L.52, B:G.53, B:K.54, B:K.54, B:K.54, B:T.55, B:T.55, B:H.56, B:K.185, B:R.210, B:R.210, C:R.161, C:R.161, C:W.164 Water bridges: B:N.23 Salt bridges: B:R.210 pi-Cation interactions: B:H.56 ANP.8: 20 residues within 4Å: Chain C: Y.12, T.16, F.17, V.18, N.23, V.50, G.51, L.52, G.53, K.54, T.55, H.56, I.181, K.185, I.209, R.210, E.213 Chain D: R.161, W.164 Ligands: MG.12 20 PLIP interactions: 17 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:Y.12, C:V.18, C:V.18, C:N.23, C:G.51, C:L.52, C:G.53, C:K.54, C:K.54, C:K.54, C:T.55, C:H.56, C:K.185, C:R.210, C:R.210, D:R.161, D:R.161, D:W.164 Salt bridges: C:R.210 pi-Stacking: C:H.56 ANP.13: 21 residues within 4Å: Chain D: Y.12, T.16, F.17, V.18, N.23, G.49, V.50, G.51, L.52, G.53, K.54, T.55, H.56, D.112, K.185, I.209, R.210, E.213 Chain E: R.161, W.164 Ligands: MG.16 22 PLIP interactions: 3 interactions with chain E, 19 interactions with chain D Hydrogen bonds: E:R.161, E:R.161, E:W.164, D:Y.12, D:V.18, D:V.18, D:N.23, D:G.51, D:L.52, D:G.53, D:K.54, D:K.54, D:K.54, D:T.55, D:T.55, D:H.56, D:D.112, D:K.185, D:R.210, D:R.210 Salt bridges: D:R.210 pi-Cation interactions: D:H.56 ANP.17: 20 residues within 4Å: Chain E: Y.12, T.16, F.17, V.18, N.23, G.49, V.50, G.51, L.52, G.53, K.54, T.55, H.56, D.112, I.181, K.185, I.209, R.210, E.213 Ligands: MG.19 17 PLIP interactions: 17 interactions with chain E Hydrogen bonds: E:Y.12, E:V.18, E:V.18, E:N.23, E:G.51, E:L.52, E:G.53, E:K.54, E:K.54, E:K.54, E:T.55, E:H.56, E:K.185, E:R.210, E:R.210 Salt bridges: E:R.210 pi-Cation interactions: E:H.56

9 x K: POTASSIUM ION(Non-covalent)

K.2: 3 residues within 4Å: Chain A: Q.123, E.124, R.157 No protein-ligand interaction detected (PLIP) K.5: 3 residues within 4Å: Chain B: E.196, N.231, A.232 No protein-ligand interaction detected (PLIP) K.6: 3 residues within 4Å: Chain B: K.119, Q.121, T.122 No protein-ligand interaction detected (PLIP) K.9: 3 residues within 4Å: Chain C: Q.123, E.124, R.157 No protein-ligand interaction detected (PLIP) K.10: 3 residues within 4Å: Chain C: K.119, Q.121, T.122 No protein-ligand interaction detected (PLIP) K.11: 1 residues within 4Å: Chain C: A.38 No protein-ligand interaction detected (PLIP) K.14: 1 residues within 4Å: Chain D: R.157 No protein-ligand interaction detected (PLIP) K.15: 4 residues within 4Å: Chain D: S.207, N.208 Chain E: D.156, R.159 No protein-ligand interaction detected (PLIP) K.18: 2 residues within 4Å: Chain E: E.124, R.157 No protein-ligand interaction detected (PLIP)

5 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: T.55, D.111, D.112 Ligands: ANP.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.55, H2O.1 MG.7: 4 residues within 4Å: Chain B: T.55, D.111, D.112 Ligands: ANP.4 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.55, H2O.1, H2O.1, H2O.1 MG.12: 4 residues within 4Å: Chain C: T.55, D.111, D.112 Ligands: ANP.8 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:T.55, H2O.2 MG.16: 3 residues within 4Å: Chain D: T.55, D.111 Ligands: ANP.13 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:T.55, H2O.4, H2O.4, H2O.4 MG.19: 4 residues within 4Å: Chain E: T.55, D.111, D.112 Ligands: ANP.17 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:T.55, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pelliciari, S. et al., The bacterial replication origin BUS promotes nucleobase capture. Nat Commun (2023)

Release Date

2023-12-13

Peptides

Chromosomal replication initiator protein DnaA: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Chromosomal replication initiator protein DnaA