SMTL ID : 8po7.1

Structure of Escherichia coli HrpA in complex with ADP and dinucleotide dCdC

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 13 residues within 4Å: Chain A: 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.2 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:E.101, A:G.103, A:S.104, A:G.105, A:K.106, A:T.107, A:T.108, A:R.141, A:T.356 Water bridges: A:K.106, A:K.106, A:T.137, A:T.137, A:R.141, A:T.353 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 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:E.101, B:G.103, B:G.103, B:S.104, B:G.105, B:G.105, B:K.106, B:T.107, B:T.107, B:T.108, B:T.356 Water bridges: B:K.106, B:K.106, B:T.137, B:T.137, B:R.141 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: 3 residues within 4Å: Chain A: T.107, E.198 Ligands: ADP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.107, H2O.1, H2O.1, H2O.2, H2O.4 MG.6: 4 residues within 4Å: Chain B: T.107, D.197, E.198 Ligands: ADP.5 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:T.107, H2O.12, H2O.13, H2O.13, H2O.14

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 3 residues within 4Å: Chain A: R.377, R.382, Q.528 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.528 Water bridges: A:R.377, A:R.382 Salt bridges: A:R.377, A:R.382

1 x DC- DC: DNA (5'-D(P*CP*C)-3')(Non-covalent)

DC-DC.4: 9 residues within 4Å: Chain B: R.26, R.29, R.30, G.33, V.34, V.37, I.46, E.49, M.50 Protein-ligand interaction information (PLIP) not available

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
B

B
A

ATP-dependent RNA helicase HrpA

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