SMTL ID : 8po8.1

Structure of Escherichia coli HrpA in complex with ADP and oligonucleotide poly(dC)11 forming an i-motif

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.52 Å

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 14 residues within 4Å: Chain A: L.77, E.101, T.102, G.103, S.104, G.105, K.106, T.107, T.108, T.137, R.141, F.336, T.356 Ligands: MG.2 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:E.101, A:G.103, A:G.103, A:S.104, A:G.105, A:K.106, A:T.107, A:T.108, A:T.356 Water bridges: A:K.106, A:K.106, A:T.107, A:D.197, A:E.198, A:E.198 Salt bridges: A:K.106 pi-Stacking: A:F.336 pi-Cation interactions: A:R.141 ADP.5: 13 residues within 4Å: Chain B: L.77, E.101, T.102, G.103, S.104, G.105, K.106, T.107, T.108, R.141, F.336, T.356 Ligands: MG.6 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:E.101, B:G.103, B:G.103, B:S.104, B:G.105, B:K.106, B:T.107, B:T.107, B:T.108, B:T.356, B:T.356 Water bridges: B:K.106, B:K.106, B:T.107, B:E.198 Salt bridges: B:K.106 pi-Stacking: B:F.336 pi-Cation interactions: B:R.141

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.107, D.197, E.198 Ligands: ADP.1 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.107, A:E.198, H2O.1, H2O.1, H2O.2 MG.6: 4 residues within 4Å: Chain B: T.107, D.197, E.198 Ligands: ADP.5 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.107, B:E.198, H2O.3, H2O.3, H2O.3

2 x SIN: SUCCINIC ACID(Non-covalent)

SIN.3: 6 residues within 4Å: Chain A: H.200, R.202, I.232, D.233, R.236, F.237 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:H.200, A:I.232, A:D.233, A:F.237 Hydrogen bonds: A:I.232, A:F.237 Salt bridges: A:R.202 SIN.4: 6 residues within 4Å: Chain A: P.130, R.131, R.132, V.158, R.159, T.174 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:R.132, A:R.159 Hydrogen bonds: A:R.132, A:R.159 Salt bridges: A:R.132, A:R.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xin, B.G. et al., Structural insights into the N-terminal APHB domain of HrpA: mediating canonical and i-motif recognition. Nucleic Acids Res. (2024)

Release Date

2024-05-08

Peptides

ATP-dependent RNA helicase HrpA: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ATP-dependent RNA helicase HrpA

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