SMTL ID : 5o1u.1

Structure of wildtype T.maritima PDE (TM1595) with AMP and Mn2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

6 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.7 MN.2: 6 residues within 4Å: Chain A: D.30, D.85, H.109, D.159 Ligands: MN.1, MN.3 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.4 MN.3: 4 residues within 4Å: Chain A: H.110, H.291 Ligands: MN.2, AMP.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.110, A:H.291, H2O.1, H2O.7 MN.5: 4 residues within 4Å: Chain B: H.24, D.28, D.85 Ligands: MN.6 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.24, B:D.28, B:D.85, H2O.14, H2O.17 MN.6: 6 residues within 4Å: Chain B: D.30, D.85, H.109, D.159 Ligands: MN.5, MN.7 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.14 MN.7: 4 residues within 4Å: Chain B: H.110, H.291 Ligands: MN.6, AMP.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.110, B:H.291, H2O.11, H2O.17

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.4: 14 residues within 4Å: Chain A: R.91, H.110, H.268, S.270, R.272, G.288, G.289, G.290, H.291, A.294, A.295, G.296, T.298 Ligands: MN.3 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.270, A:S.270, A:G.289, A:T.298, A:T.298 Water bridges: A:S.87, A:R.91, A:R.91, A:T.298 Salt bridges: A:H.268, A:R.272 pi-Cation interactions: A:R.91, A:R.91 AMP.9: 17 residues within 4Å: Chain B: D.28, R.91, H.110, H.268, V.269, S.270, R.272, G.288, G.289, G.290, H.291, A.294, A.295, G.296, V.297, T.298 Ligands: MN.7 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:S.270, B:G.289, B:T.298, B:T.298, B:T.298 Water bridges: B:S.87, B:R.91, B:R.91, B:R.91, B:R.91, B:R.91, B:D.159, B:S.270 Salt bridges: B:H.268, B:R.272 pi-Cation interactions: B:R.91, B:R.91

1 x CA: CALCIUM ION(Non-covalent)

CA.8: 2 residues within 4Å: Chain B: D.90, G.287 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:G.287, H2O.18

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

EDO.10: 8 residues within 4Å: Chain A: R.251, G.252, K.274 Chain B: K.63, K.191, E.192, E.195, N.196 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.252, A:K.274, A:K.274, B:K.63, B:E.192

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Phosphodiesterase

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