SMTL ID : 4lrl.3 (2 other biounits)

Structure of an Enterococcus Faecalis HD-domain protein complexed with dGTP and dTTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

2 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 4 residues within 4Å: Chain A: H.90, H.134, D.135, D.207 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.90, A:H.134, A:D.135, A:D.207, H2O.6 NI.4: 4 residues within 4Å: Chain B: H.90, H.134, D.135, D.207 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.90, B:H.134, B:D.135, B:D.207, H2O.12

2 x DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DGT.2: 14 residues within 4Å: Chain A: K.38, V.39, F.40, I.59, N.60, Q.65, R.68, F.88 Chain B: F.78, T.79, V.271, R.350, K.354, K.446 21 PLIP interactions: 11 interactions with chain B, 10 interactions with chain A Hydrogen bonds: B:R.350, A:N.60, A:N.60, A:N.60, A:Q.65, A:R.68 Water bridges: B:R.350, B:R.350, B:K.354, B:K.354, B:K.446, A:R.41 Salt bridges: B:R.350, B:K.354, B:K.354, B:K.446, A:K.38, A:K.38, A:K.38 pi-Cation interactions: B:R.350 Hydrophobic interactions: A:F.40 DGT.5: 16 residues within 4Å: Chain A: F.78, T.79, V.271, R.350, K.354, K.446 Chain B: K.38, V.39, F.40, L.56, I.59, N.60, Q.65, R.68, F.88 Ligands: TTP.6 18 PLIP interactions: 11 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:F.40 Hydrogen bonds: B:K.38, B:K.38, B:N.60, B:N.60, B:N.60, B:Q.65, B:R.68 Salt bridges: B:K.38, B:K.38, B:K.38, A:R.350, A:K.354, A:K.354, A:K.446 Water bridges: A:R.350, A:R.350 pi-Cation interactions: A:R.350

1 x MLI: MALONATE ION(Non-functional Binders)

MLI.3: 4 residues within 4Å: Chain A: V.378, G.379, F.380, Y.385 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.380

1 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.6: 9 residues within 4Å: Chain A: T.79, F.80, Q.265, H.269 Chain B: K.38, V.39, F.40, R.41 Ligands: DGT.5 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.80 Water bridges: A:Q.265, A:H.269, A:H.269 Salt bridges: A:H.269, B:K.38 Hydrogen bonds: B:R.41, B:R.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vorontsov, I.I. et al., Mechanisms of Allosteric Activation and Inhibition of the Deoxyribonucleoside Triphosphate Triphosphohydrolase from Enterococcus faecalis. J.Biol.Chem. (2014)

Release Date

2013-11-20

Peptides

HD domain protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

HD domain protein

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