SMTL ID : 5o58.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

1 x A- G: RNA (5'-R(P*AP*G)-3')(Non-covalent)

A-G.1: 24 residues within 4Å: Chain A: H.109, H.110, T.158, N.159, G.161, H.165, N.167, R.248, H.268, S.270, R.272, G.288, G.289, G.290, H.291, R.293, A.294, A.295, G.296, V.297, T.298 Ligands: IPA.21, CL.25, CL.26 Protein-ligand interaction information (PLIP) not available

18 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 4 residues within 4Å: Chain A: E.200, K.203, R.232, H.233 Ligand excluded by PLIP EDO.3: 5 residues within 4Å: Chain A: W.276, F.277, N.278, E.281, K.318 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: K.44, Y.66, D.145, N.147, L.148 Ligands: EDO.10 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: K.197, R.198, F.199, E.200 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: G.252, V.253, E.254, K.274, D.275 Ligand excluded by PLIP EDO.7: 2 residues within 4Å: Chain A: S.166, A.168 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: K.138, V.142, E.143, Y.144, M.182 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: F.134, R.135, K.138, D.175, K.178 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: L.40, E.43, K.44 Ligands: EDO.4 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: M.26, Y.55, T.236, D.237, E.238, F.262 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: P.65, Y.66 Ligands: EDO.14 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: F.299, K.302, E.306, R.310 Ligands: IPA.23 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: Y.66, D.68, K.69 Ligands: EDO.12 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: D.17, R.18, E.48 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain A: S.111, P.124, G.290, H.291, P.292 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: D.123, S.125, F.126, R.171 Ligand excluded by PLIP EDO.18: 2 residues within 4Å: Chain A: N.118, W.119 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain A: E.174, Y.177, K.178 Ligand excluded by PLIP

5 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.20: 8 residues within 4Å: Chain A: S.125, F.126, A.127, Q.131, N.167, D.169, R.171, V.172 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.126, A:A.127 Hydrogen bonds: A:R.171, A:R.171 Water bridges: A:R.171 IPA.21: 5 residues within 4Å: Chain A: G.242, R.272 Ligands: A-G.1, A-G.1, CL.25 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.272 Water bridges: A:S.270 IPA.22: 5 residues within 4Å: Chain A: K.197, Q.201, F.202, F.205, F.243 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.202, A:F.205, A:F.205 IPA.23: 3 residues within 4Å: Chain A: L.286, F.299 Ligands: EDO.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.286 Hydrogen bonds: A:L.286 IPA.24: 4 residues within 4Å: Chain A: K.94, F.95, D.97, L.98 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.94, A:D.97

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

CL.25: 6 residues within 4Å: Chain A: G.242, V.244, G.245, R.272 Ligands: A-G.1, IPA.21 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain A: S.166, N.167 Ligands: A-G.1 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

phosphodiesterase TM1595: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

phosphodiesterase TM1595

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