SMTL ID : 3qvq.1 (1 other biounit)

The structure of an Oleispira antarctica phosphodiesterase OLEI02445 in complex with the product sn-glycerol-3-phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x G3P: SN-GLYCEROL-3-PHOSPHATE(Non-covalent)

G3P.1: 11 residues within 4Å: Chain A: H.15, R.16, E.42, D.44, H.57, E.117, F.151, N.171, F.216, F.236 Ligands: MG.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:E.117, A:E.117, A:N.171 Water bridges: A:R.16, A:R.16, A:H.57, A:K.119 Salt bridges: A:H.15, A:R.16, A:H.57, A:K.119 G3P.17: 11 residues within 4Å: Chain B: H.15, R.16, E.42, D.44, H.57, E.117, F.151, N.171, F.216, T.217 Ligands: MG.18 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:E.117, B:N.171 Water bridges: B:H.15, B:R.16, B:R.16 Salt bridges: B:H.15, B:R.16, B:H.57, B:K.119

7 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 4 residues within 4Å: Chain A: E.42, D.44, E.117 Ligands: G3P.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.42, A:D.44, A:E.117, H2O.1 MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Chain A: E.91 No protein-ligand interaction detected (PLIP) MG.18: 4 residues within 4Å: Chain B: E.42, D.44, E.117 Ligands: G3P.17 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.42, B:D.44, B:E.117, H2O.11 MG.19: 3 residues within 4Å: Chain B: S.62, T.65, D.66 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.62, B:T.65, H2O.12, H2O.12, H2O.14, H2O.18 MG.20: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.21: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

5 x NA: SODIUM ION(Non-functional Binders)

NA.5: 4 residues within 4Å: Chain A: S.196, F.197, F.198 Chain B: K.73 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:F.198, B:K.73 NA.6: 1 residues within 4Å: Chain A: Q.195 No protein-ligand interaction detected (PLIP) NA.7: 2 residues within 4Å: Chain A: E.91 Ligands: EDO.15 No protein-ligand interaction detected (PLIP) NA.8: 3 residues within 4Å: Chain A: G.49, K.73, P.75 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.49 NA.22: 5 residues within 4Å: Chain B: A.167, R.168, D.187, C.188, A.189 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.168, B:D.187, B:A.189 Water bridges: B:R.168

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

CL.9: 5 residues within 4Å: Chain A: Y.60, L.61, S.62, D.68, G.69 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: W.163, P.164, E.165 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: P.10, Q.11 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain A: Q.195, I.218, N.219, D.220 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain A: G.89, Q.90 Ligand excluded by PLIP CL.23: 5 residues within 4Å: Chain B: Q.36, Y.239, P.240, Q.241, K.242 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain B: Q.195, I.218, N.219, D.220 Ligand excluded by PLIP

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

PEG.14: 4 residues within 4Å: Chain A: E.184, A.209, G.210, Y.211 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.210

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

EDO.15: 4 residues within 4Å: Chain A: Q.21, E.91, Y.92 Ligands: NA.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.21 Water bridges: A:E.91

1 x NI: NICKEL (II) ION(Non-covalent)

NI.16: 2 residues within 4Å: Chain A: Q.138, H.139 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.139, H2O.5, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singer, A.U. et al., The structure of an Oleispira antarctica phosphodiesterase OLEI02445 in complex with the product sn-glycerol-3-phosphate. To be Published

Release Date

2011-04-13

Peptides

Phosphodiesterase Olei02445: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Phosphodiesterase Olei02445

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