SMTL ID : 6fws.1

Structure of DinG in complex with ssDNA and ADPBeF

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 5 residues within 4Å: Chain A: R.115, C.120, P.121, R.122, C.205 2 PLIP interactions: 2 interactions with chain A, Metal complexes: A:C.120, A:C.205 SF4.5: 6 residues within 4Å: Chain C: R.115, C.120, P.121, R.122, C.205, F.208 2 PLIP interactions: 2 interactions with chain C, Metal complexes: C:C.120, C:C.205

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

ADP.2: 18 residues within 4Å: Chain A: I.22, D.24, F.25, I.26, R.28, Q.31, T.56, G.57, V.58, G.59, K.60, T.61, K.95, D.599, K.601, R.659 Ligands: BEF.3, MG.4 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:I.26, A:R.28, A:R.28, A:Q.31, A:Q.31, A:G.57, A:G.59, A:K.60, A:T.61, A:T.61, A:T.61, A:K.95, A:K.95, A:D.599, A:K.601 Water bridges: A:E.249, A:R.659, A:R.659 Salt bridges: A:K.60, A:R.659, A:R.659 pi-Cation interactions: A:R.28, A:R.28 ADP.6: 17 residues within 4Å: Chain C: F.25, I.26, R.28, Q.31, T.56, G.57, V.58, G.59, K.60, T.61, L.62, K.95, D.599, K.601, R.659 Ligands: BEF.7, MG.8 21 PLIP interactions: 21 interactions with chain C Hydrogen bonds: C:I.26, C:R.28, C:R.28, C:Q.31, C:Q.31, C:G.57, C:G.59, C:K.60, C:T.61, C:T.61, C:K.95, C:K.95, C:D.599, C:K.601 Water bridges: C:K.60, C:Q.91, C:R.659 Salt bridges: C:K.60, C:R.659, C:R.659 pi-Cation interactions: C:R.28

2 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.3: 10 residues within 4Å: Chain A: T.56, G.57, K.60, E.249, A.460, G.597, R.656, R.659 Ligands: ADP.2, MG.4 No protein-ligand interaction detected (PLIP) BEF.7: 11 residues within 4Å: Chain C: T.56, G.57, K.60, E.249, A.460, E.596, Q.652, R.656, R.659 Ligands: ADP.6, MG.8 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: E.249 Ligands: ADP.2, BEF.3 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain C: E.249 Ligands: ADP.6, BEF.7 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cheng, K. et al., DNA translocation mechanism of an XPD family helicase. Elife (2018)

Release Date

2018-12-19

Peptides

ATP-dependent DNA helicase DinG: AC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

ATP-dependent DNA helicase DinG

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