SMTL ID : 5o4z.1

Structure of the inactive T.maritima PDE (TM1595) D80N D154N mutant with substrate 5'-pApA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

4 x A: ADENOSINE-5'-MONOPHOSPHATE(Non-covalent)

A.1: 15 residues within 4Å: Chain A: H.110, H.268, S.270, R.272, G.288, G.289, G.290, H.291, A.294, A.295, G.296, V.297, T.298 Ligands: A.2, GOL.9 45 PLIP interactions: 23 interactions with chain A, 22 interactions with chain B Hydrogen bonds: A:T.158, A:N.159, A:G.161, A:S.166, A:S.166, A:S.270, A:S.270, A:T.298, A:T.298, A:T.298, B:T.158, B:N.159, B:G.161, B:S.166, B:S.166, B:S.270, B:S.270, B:T.298, B:T.298 Water bridges: A:N.85, A:T.112, A:N.159, A:R.248, A:S.270, A:R.293, A:R.293, B:D.28, B:N.85, B:N.159, B:R.248, B:S.270, B:R.293, B:R.293 Salt bridges: A:H.109, A:H.110, A:H.268, A:R.272, A:H.291, B:H.109, B:H.110, B:H.268, B:R.272, B:H.291 pi-Stacking: A:H.165, B:H.165 A.2: 15 residues within 4Å: Chain A: H.109, H.110, T.158, N.159, G.161, H.165, S.166, N.167, R.248, R.272, H.291, R.293, A.294 Ligands: A.1, SO4.7 Protein-ligand interaction information (PLIP) not available A.13: 15 residues within 4Å: Chain B: H.110, H.268, S.270, R.272, G.288, G.289, G.290, H.291, A.294, A.295, G.296, V.297, T.298 Ligands: A.14, GOL.21 Protein-ligand interaction information (PLIP) not available A.14: 15 residues within 4Å: Chain B: H.109, H.110, T.158, N.159, G.161, H.165, S.166, N.167, R.248, R.272, H.291, R.293, A.294 Ligands: A.13, SO4.19 Protein-ligand interaction information (PLIP) not available

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain A: E.71, E.72, N.73 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.72, A:N.73, A:N.73 Water bridges: A:E.71 SO4.4: 2 residues within 4Å: Chain A: R.135, R.171 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.135, A:R.135 Salt bridges: A:R.135, A:R.171 SO4.5: 2 residues within 4Å: Chain A: D.145, S.146 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.146 SO4.6: 7 residues within 4Å: Chain A: K.197, F.202, F.205, F.243, E.246 Chain B: E.246 Ligands: SO4.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.246 Water bridges: A:K.197 Salt bridges: A:K.197 SO4.7: 7 residues within 4Å: Chain A: R.164, H.165, G.242, G.245, R.248, R.272 Ligands: A.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.164, A:G.245 Water bridges: A:G.242, A:G.242 Salt bridges: A:H.165, A:R.248, A:R.272 SO4.8: 5 residues within 4Å: Chain A: L.286, G.287, V.297, T.298, F.299 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.298, A:E.300 SO4.15: 3 residues within 4Å: Chain B: E.71, E.72, N.73 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.72, B:N.73, B:N.73 SO4.16: 2 residues within 4Å: Chain B: R.135, R.171 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.135, B:R.135 Salt bridges: B:R.135, B:R.171 SO4.17: 2 residues within 4Å: Chain B: D.145, S.146 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.145, B:S.146 SO4.18: 7 residues within 4Å: Chain A: E.246 Chain B: K.197, F.202, F.205, F.243, E.246 Ligands: SO4.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.246 Water bridges: B:K.197 Salt bridges: B:K.197 SO4.19: 7 residues within 4Å: Chain B: R.164, H.165, G.242, G.245, R.248, R.272 Ligands: A.14 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.164, B:G.245 Water bridges: B:G.242, B:G.242 Salt bridges: B:H.165, B:R.248, B:R.272 SO4.20: 5 residues within 4Å: Chain B: L.286, G.287, V.297, T.298, F.299 2 PLIP interactions: 2 interactions with chain B Water bridges: B:T.298, B:E.300

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 2 residues within 4Å: Chain A: R.91 Ligands: A.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.87 Water bridges: A:S.87, A:S.88, A:S.88 GOL.10: 2 residues within 4Å: Chain A: Y.224, E.305 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.222 GOL.21: 2 residues within 4Å: Chain B: R.91 Ligands: A.13 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.87 Water bridges: B:S.87, B:S.88, B:S.88 GOL.22: 2 residues within 4Å: Chain B: Y.224, E.305 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.305 Water bridges: B:Y.222, B:Y.222

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 2 residues within 4Å: Chain A: P.65, Y.66 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain A: S.111, H.291 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain B: P.65, Y.66 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain B: S.111, H.291 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Drexler, D.J. et al., Structural and Biophysical Analysis of the Soluble DHH/DHHA1-Type Phosphodiesterase TM1595 from Thermotoga maritima. Structure (2017)

Release Date

2017-10-25

Peptides

DHH/DHHA1-type phosphodiesterase TM1595: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

DHH/DHHA1-type phosphodiesterase TM1595

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