SMTL ID : 5o25.1

Structure of wildtype T.maritima PDE (TM1595) in ligand-free state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: H.24, D.28, D.85 Ligands: MN.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.24, A:D.28, A:D.85, H2O.4, H2O.8 MN.2: 5 residues within 4Å: Chain A: D.30, D.85, H.109, D.159 Ligands: MN.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.30, A:D.85, A:H.109, A:D.159, H2O.7 MN.12: 6 residues within 4Å: Chain B: H.24, D.28, D.30, C.31, D.85 Ligands: MN.13 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.24, B:D.28, B:D.85, H2O.13, H2O.15 MN.13: 6 residues within 4Å: Chain B: D.30, D.85, H.109, H.110, D.159 Ligands: MN.12 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.30, B:D.85, B:H.109, B:D.159, H2O.13

3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 15 residues within 4Å: Chain A: M.26, R.91, H.110, M.260, H.268, S.270, R.272, G.289, G.290, H.291, A.294, A.295, G.296, V.297, T.298 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.272, A:R.272 PG4.14: 9 residues within 4Å: Chain A: F.205, E.246 Chain B: K.197, Q.201, F.202, F.205, G.242, F.243, E.246 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.246 Water bridges: B:G.242, B:G.242 PG4.15: 5 residues within 4Å: Chain B: D.237, F.262, P.263, K.266, T.298 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.266

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 5 residues within 4Å: Chain A: L.286, F.299, V.307, R.310 Ligands: PEG.5 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.303, A:E.306 PEG.5: 4 residues within 4Å: Chain A: L.286, R.310, H.314 Ligands: PEG.4 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.310 PEG.6: 3 residues within 4Å: Chain A: N.313, K.317, K.320 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.320 PEG.7: 3 residues within 4Å: Chain A: Y.222, Y.224, I.308 No protein-ligand interaction detected (PLIP) PEG.8: 8 residues within 4Å: Chain A: K.197, Q.201, F.202, F.205, G.242, F.243, E.246 Chain B: E.246 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.246, A:K.197 PEG.9: 3 residues within 4Å: Chain A: P.65, Y.66, N.147 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.66, A:N.147

2 x CA: CALCIUM ION(Non-covalent)

CA.10: 2 residues within 4Å: Chain B: D.17, G.46 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:G.46, H2O.12, H2O.15 CA.11: 1 residues within 4Å: Chain B: E.62 No protein-ligand interaction detected (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

TmPDE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

TmPDE

Related Entries With Identical Sequence