SMTL ID : 3r8f.1

Replication initiator DnaA bound to AMPPCP and single-stranded DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.37 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: T.51, D.105, D.106 Ligands: ACP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.51 MG.3: 4 residues within 4Å: Chain B: T.51, D.105, D.106 Ligands: ACP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.51 MG.5: 4 residues within 4Å: Chain C: T.51, D.105, D.106 Ligands: ACP.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.51 MG.7: 4 residues within 4Å: Chain D: T.51, D.105, D.106 Ligands: ACP.8 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.51

4 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.2: 17 residues within 4Å: Chain A: Y.8, N.12, F.13, I.14, N.19, V.46, G.47, T.48, G.49, K.50, T.51, H.52, K.178, V.201, R.202, E.205 Ligands: MG.1 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:Y.8, A:Y.8, A:I.14, A:I.14, A:T.48, A:G.49, A:K.50, A:K.50, A:T.51, A:T.51, A:H.52, A:K.178, A:R.202, A:R.202 Salt bridges: A:R.202 pi-Stacking: A:H.52 ACP.4: 19 residues within 4Å: Chain A: R.155 Chain B: Y.8, N.12, F.13, I.14, N.19, V.46, G.47, T.48, G.49, K.50, T.51, H.52, D.106, K.178, V.201, R.202, E.205 Ligands: MG.3 19 PLIP interactions: 17 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.8, B:Y.8, B:I.14, B:I.14, B:N.19, B:T.48, B:G.49, B:K.50, B:K.50, B:K.50, B:T.51, B:H.52, B:D.106, B:K.178, B:R.202, B:R.202, A:R.155, A:R.155 pi-Stacking: B:H.52 ACP.6: 18 residues within 4Å: Chain B: R.155 Chain C: Y.8, N.12, F.13, I.14, N.19, V.46, G.47, T.48, G.49, K.50, T.51, H.52, K.178, V.201, R.202, E.205 Ligands: MG.5 17 PLIP interactions: 15 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:Y.8, C:I.14, C:I.14, C:T.48, C:G.49, C:K.50, C:K.50, C:K.50, C:T.51, C:H.52, C:K.178, C:R.202, C:R.202, B:R.155, B:R.155 Salt bridges: C:R.202 pi-Stacking: C:H.52 ACP.8: 19 residues within 4Å: Chain C: R.155 Chain D: Y.8, N.12, F.13, I.14, N.19, V.46, G.47, T.48, G.49, K.50, T.51, H.52, D.106, K.178, V.201, R.202, E.205 Ligands: MG.7 17 PLIP interactions: 15 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:Y.8, D:I.14, D:I.14, D:T.48, D:G.49, D:K.50, D:K.50, D:K.50, D:T.51, D:H.52, D:K.178, D:R.202, D:R.202, C:R.155, C:R.155 Salt bridges: D:R.202 pi-Stacking: D:H.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Duderstadt, K.E. et al., DNA stretching by bacterial initiators promotes replication origin opening. Nature (2011)

Release Date

2011-09-28

Peptides

Chromosomal replication initiator protein dnaA: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Chromosomal replication initiator protein dnaA

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