SMTL ID : 5o7f.1

Structure of the inactive T.maritima PDE (TM1595) D80N D154N mutant with GMP and Mn2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x 5GP: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

5GP.1: 17 residues within 4Å: Chain A: S.87, R.91, 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: MN.3, EDO.6 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:S.87, A:S.87, A:S.270, A:S.270, A:G.289, A:G.289 Water bridges: A:R.91, A:R.91, A:R.272, A:T.298, A:T.298 Salt bridges: A:H.268, A:R.272 pi-Cation interactions: A:R.91, A:R.91 5GP.8: 16 residues within 4Å: Chain B: S.87, R.91, 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: MN.10 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:S.87, B:S.87, B:S.270, B:G.289, B:T.298, B:T.298 Water bridges: B:R.91, B:R.91, B:R.91, B:R.91, B:N.159, B:R.272 Salt bridges: B:H.268, B:R.272 pi-Cation interactions: B:R.91, B:R.91

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

MN.2: 4 residues within 4Å: Chain A: H.24, D.28, C.31, N.85 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.24, A:D.28, A:D.28, H2O.6, H2O.6 MN.3: 3 residues within 4Å: Chain A: H.110, H.291 Ligands: 5GP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.110, A:H.291, H2O.6, H2O.6 MN.9: 4 residues within 4Å: Chain B: H.24, D.28, C.31, N.85 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.24, B:D.28, B:D.28, H2O.17, H2O.18 MN.10: 3 residues within 4Å: Chain B: H.110, H.291 Ligands: 5GP.8 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.110, B:H.291, H2O.17, H2O.18

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

EDO.4: 6 residues within 4Å: Chain A: R.251 Chain B: Y.59, N.196, R.198, E.238, D.239 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:R.251, A:R.251 Water bridges: B:N.196, B:R.198, B:Q.201, B:E.238 EDO.5: 5 residues within 4Å: Chain A: F.202, F.205 Chain B: F.202, F.205, L.209 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:F.202, B:F.202 EDO.6: 7 residues within 4Å: Chain A: S.87, S.88, T.112, T.114, G.288, G.289 Ligands: 5GP.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.87, A:T.112, A:T.112, A:G.288 Water bridges: A:G.290 EDO.7: 4 residues within 4Å: Chain A: R.198, F.199 Chain B: I.250, R.251 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:F.199 Water bridges: B:R.251 EDO.11: 6 residues within 4Å: Chain A: I.250, R.251 Chain B: K.197, R.198, F.199, E.200 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.199 EDO.12: 3 residues within 4Å: Chain B: D.17, R.18, E.48 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.48 Water bridges: B:D.17, B:R.18

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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