SMTL ID : 2hcb.1

Structure of AMPPCP-bound DnaA from Aquifex aeolicus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.51 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: T.50, D.104, D.105 Ligands: ACP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.50, A:D.105 MG.3: 3 residues within 4Å: Chain B: T.50, D.105 Ligands: ACP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.50 MG.5: 5 residues within 4Å: Chain C: K.49, T.50, D.104, D.105 Ligands: ACP.6 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.50, C:D.105 MG.7: 5 residues within 4Å: Chain D: K.49, T.50, D.104, D.105 Ligands: ACP.8 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.50

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

ACP.2: 18 residues within 4Å: Chain A: Y.7, N.11, F.12, I.13, N.18, V.45, G.46, T.47, G.48, K.49, T.50, H.51, D.105, K.177, V.200, R.201, E.204 Ligands: MG.1 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:Y.7, A:I.13, A:I.13, A:G.46, A:T.47, A:G.48, A:K.49, A:K.49, A:T.50, A:H.51, A:K.177, A:R.201, A:R.201 Salt bridges: A:R.201 pi-Cation interactions: A:H.51 ACP.4: 20 residues within 4Å: Chain A: R.154 Chain B: Y.7, N.11, F.12, I.13, N.18, S.44, V.45, G.46, T.47, G.48, K.49, T.50, H.51, D.105, K.177, V.200, R.201, E.204 Ligands: MG.3 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:I.13, B:I.13, B:G.46, B:T.47, B:G.48, B:K.49, B:K.49, B:K.49, B:T.50, B:T.50, B:H.51, B:K.177, B:R.201, B:R.201, A:R.154, A:R.154 Salt bridges: B:R.201 pi-Stacking: B:H.51 ACP.6: 19 residues within 4Å: Chain B: R.154 Chain C: Y.7, N.11, F.12, I.13, N.18, V.45, G.46, T.47, G.48, K.49, T.50, H.51, D.105, K.177, V.200, R.201, E.204 Ligands: MG.5 17 PLIP interactions: 15 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:I.13, C:I.13, C:G.46, C:T.47, C:G.48, C:K.49, C:K.49, C:K.49, C:T.50, C:T.50, C:H.51, C:K.177, C:R.201, C:R.201, B:R.154, B:R.154 Salt bridges: C:R.201 ACP.8: 19 residues within 4Å: Chain C: R.154 Chain D: Y.7, N.11, F.12, I.13, N.18, V.45, G.46, T.47, G.48, K.49, T.50, H.51, D.105, K.177, V.200, R.201, E.204 Ligands: MG.7 17 PLIP interactions: 15 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:I.13, D:I.13, D:G.46, D:T.47, D:G.48, D:K.49, D:K.49, D:K.49, D:T.50, D:H.51, D:K.177, D:R.201, D:R.201, C:R.154, C:R.154 Salt bridges: D:R.201 pi-Cation interactions: D:H.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Erzberger, J.P. et al., Structural basis for ATP-dependent DnaA assembly and replication-origin remodeling. Nat.Struct.Mol.Biol. (2006)

Release Date

2006-07-25

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