SMTL ID : 2is6.1

Crystal structure of UvrD-DNA-ADPMgF3 ternary complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain C: T.36, E.221 Ligands: MGF.2, ADP.3 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.36, H2O.7, H2O.7, H2O.7 MG.5: 5 residues within 4Å: Chain D: T.36, D.220, E.221 Ligands: MGF.6, ADP.7 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:T.36, H2O.12, H2O.14, H2O.14

2 x MGF: TRIFLUOROMAGNESATE(Non-covalent)

MGF.2: 10 residues within 4Å: Chain C: A.31, G.32, K.35, E.221, Q.251, R.284, G.564, R.605 Ligands: MG.1, ADP.3 No protein-ligand interaction detected (PLIP) MGF.6: 11 residues within 4Å: Chain D: A.31, G.32, K.35, T.36, E.221, Q.251, R.284, G.564, R.605 Ligands: MG.5, ADP.7 No protein-ligand interaction detected (PLIP)

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

ADP.3: 16 residues within 4Å: Chain C: S.9, L.10, Q.14, A.31, G.32, S.33, G.34, K.35, T.36, R.37, R.73, Y.283, R.284, E.566 Ligands: MG.1, MGF.2 25 PLIP interactions: 25 interactions with chain C Hydrogen bonds: C:S.9, C:Q.14, C:G.32, C:S.33, C:G.34, C:K.35, C:T.36, C:R.37, C:R.37, C:E.566 Water bridges: C:T.36, C:T.36, C:R.37, C:R.73, C:R.73, C:E.221, C:G.564 Salt bridges: C:K.35, C:R.73, C:R.284, C:R.284 pi-Stacking: C:Y.283, C:Y.283 pi-Cation interactions: C:R.37, C:R.37 ADP.7: 16 residues within 4Å: Chain D: S.9, L.10, Q.14, A.31, G.32, S.33, G.34, K.35, T.36, R.37, R.73, Y.283, R.284, E.566 Ligands: MG.5, MGF.6 25 PLIP interactions: 25 interactions with chain D Hydrogen bonds: D:Q.14, D:Q.14, D:G.32, D:S.33, D:G.34, D:K.35, D:T.36, D:R.37, D:R.37, D:E.566 Water bridges: D:T.36, D:R.37, D:R.73, D:R.73, D:R.73, D:E.221, D:E.566, D:R.605 Salt bridges: D:K.35, D:R.73, D:R.284, D:R.284 pi-Stacking: D:Y.283 pi-Cation interactions: D:R.37, D:R.37

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain C: K.65, Q.555, L.565, E.566, F.567 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.65 Water bridges: C:E.69, C:E.566

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, J.Y. et al., UvrD helicase unwinds DNA one base pair at a time by a two-part power stroke. Cell(Cambridge,Mass.) (2006)

Release Date

2007-01-09

Peptides

DNA helicase II: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

D
B

DNA helicase II

Related Entries With Identical Sequence