SMTL ID : 3irh.1 (4 other biounits)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.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.3 CA.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.8 CA.6: 4 residues within 4Å: Chain C: H.90, H.134, D.135, D.207 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.90, C:H.134, C:D.135, C:D.207 CA.9: 4 residues within 4Å: Chain D: H.90, H.134, D.135, D.207 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.90, D:H.134, D:D.135, D:D.207, H2O.15

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

DGT.2: 14 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, I.59, N.60, Q.65, R.68, F.88 19 PLIP interactions: 9 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:F.40 Hydrogen bonds: B:N.60, B:N.60, B:N.60, B:Q.65, B:R.68, A:R.350 Salt bridges: B:K.38, B:K.38, B:K.38, A:R.350, A:K.354, A:K.354, A:K.354, A:K.446 Water bridges: A:R.350, A:R.350, A:R.350 pi-Cation interactions: A:R.350 DGT.3: 14 residues within 4Å: Chain A: K.38, V.39, F.40, L.56, I.59, N.60, Q.65, R.68, F.88 Chain B: F.78, T.79, V.271, R.350, K.354 18 PLIP interactions: 10 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:F.40 Hydrogen bonds: A:N.60, A:N.60, A:N.60, A:Q.65, A:R.68 Water bridges: A:V.39, B:R.350, B:R.350, B:R.350 Salt bridges: A:K.38, A:K.38, A:K.38, B:R.350, B:K.354, B:K.354, B:K.446 pi-Cation interactions: B:R.350 DGT.7: 14 residues within 4Å: Chain C: F.78, T.79, V.271, R.350, K.354, K.446 Chain D: K.38, V.39, F.40, I.59, N.60, Q.65, R.68, F.88 21 PLIP interactions: 11 interactions with chain D, 10 interactions with chain C Hydrophobic interactions: D:F.40 Hydrogen bonds: D:N.60, D:N.60, D:N.60, D:Q.65, D:R.68, C:R.350 Water bridges: D:K.38, D:K.38, C:H.269, C:R.350, C:R.350, C:R.350 Salt bridges: D:K.38, D:K.38, D:K.38, C:R.350, C:K.354, C:K.354, C:K.446 pi-Cation interactions: C:R.350 DGT.8: 15 residues within 4Å: Chain C: K.38, V.39, F.40, L.56, I.59, N.60, Q.65, R.68, F.88 Chain D: F.78, T.79, V.271, R.350, K.354, K.446 18 PLIP interactions: 9 interactions with chain C, 9 interactions with chain D Hydrophobic interactions: C:F.40 Hydrogen bonds: C:N.60, C:N.60, C:N.60, C:Q.65, C:R.68, D:R.350 Salt bridges: C:K.38, C:K.38, C:K.38, D:R.350, D:K.354, D:K.446 Water bridges: D:R.350, D:K.446, D:K.446 pi-Cation interactions: D:R.350, D:R.350

2 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.5: 11 residues within 4Å: Chain B: Q.72, L.73, S.76, R.87, H.138, H.143, H.153, Y.211, Y.263, Y.267, Y.392 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.392 Hydrogen bonds: B:Q.72, B:H.143, B:Y.211, B:Y.392 Water bridges: B:Y.211, B:Y.211 Salt bridges: B:R.87, B:H.138, B:H.138, B:H.143, B:H.153 pi-Cation interactions: B:H.143 DTP.10: 11 residues within 4Å: Chain D: L.73, S.76, R.87, D.135, H.138, H.143, Y.211, Y.263, Y.267, Y.392, D.393 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:Y.392 Hydrogen bonds: D:R.87, D:D.135, D:Y.211, D:Y.263, D:D.393 Water bridges: D:T.75, D:T.75 Salt bridges: D:H.138, D:H.143, D:H.143

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vorontsov, I.I. et al., Characterization of the deoxynucleotide triphosphate triphosphohydrolase (dNTPase) activity of the EF1143 protein from Enterococcus faecalis and crystal structure of the activator-substrate complex. J.Biol.Chem. (2011)

Release Date

2009-09-22

Peptides

HD domain protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

HD domain protein

Related Entries With Identical Sequence