SMTL ID : 5v9x.1

Structure of Mycobacterium smegmatis helicase Lhr bound to ssDNA and AMP-PNP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

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

ANP.1: 19 residues within 4Å: Chain A: F.41, F.45, A.47, P.48, T.49, Q.52, P.70, T.71, G.74, K.75, T.76, E.192, G.388, D.390, R.415, H.418, V.420 Ligands: GOL.5, MG.6 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:A.47, A:T.49, A:Q.52, A:T.71, A:S.73, A:G.74, A:K.75, A:K.75, A:K.75, A:T.76, A:T.76, A:T.76, A:D.390, A:R.415, A:R.415 Salt bridges: A:H.418

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: V.111, R.115, A.365, E.368, D.369 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.115, A:D.369, A:D.369 GOL.3: 9 residues within 4Å: Chain A: K.107, A.108, V.111, D.146, H.355, K.361, R.364, A.365, E.368 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.364 GOL.4: 2 residues within 4Å: Chain A: S.373, R.375 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.375 GOL.5: 5 residues within 4Å: Chain A: T.76, L.77, N.116, D.390 Ligands: ANP.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.77, A:N.116, A:N.116

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 4 residues within 4Å: Chain A: K.75, D.191, E.192 Ligands: ANP.1 No protein-ligand interaction detected (PLIP)

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 6 residues within 4Å: Chain A: T.199, K.200, R.201, A.548, I.549 Chain B: T.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.199, A:R.201

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ejaz, A. et al., Structure of mycobacterial 3'-to-5' RNA:DNA helicase Lhr bound to a ssDNA tracking strand highlights distinctive features of a novel family of bacterial helicases. Nucleic Acids Res. (2018)

Release Date

2017-12-06

Peptides

ATP-dependent DNA helicase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ATP-dependent DNA helicase