SMTL ID : 3qvq.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

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

G3P.1: 12 residues within 4Å: Chain A: H.15, R.16, E.42, D.44, H.57, E.117, K.119, F.151, N.171, F.216, F.236 Ligands: MG.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.42, A:E.42, A:N.171 Water bridges: A:K.119 Salt bridges: A:H.15, A:R.16, A:H.57, A:K.119 G3P.14: 12 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, F.236 Ligands: MG.15 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.42, B:N.171 Water bridges: B:H.15, B:E.42, B:D.44 Salt bridges: B:H.15, B:R.16, B:H.57

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: E.42, D.44, E.117 Ligands: G3P.1 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:E.42, A:D.44, A:E.117, H2O.1, G3P.1 MG.3: 1 residues within 4Å: Chain A: D.205 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Chain A: E.91 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain A: D.59, E.122 Chain B: S.173 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.59, A:E.122, H2O.3 MG.15: 4 residues within 4Å: Chain B: E.42, D.44, E.117 Ligands: G3P.14 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.42, B:D.44, B:E.117, H2O.9 MG.16: 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.10, H2O.11, H2O.14, H2O.14

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

NA.6: 6 residues within 4Å: Chain A: F.148, A.159, K.160, W.163, I.166, R.168 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.159, A:R.168 NA.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

CL.7: 5 residues within 4Å: Chain A: Y.60, L.61, S.62, D.68, G.69 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: P.10, Q.11 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: Q.195, I.218, N.219, D.220 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: S.4, A.5, Y.6, A.167 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain A: P.53, T.99, L.100, L.101, V.135 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain A: K.226 Ligand excluded by PLIP CL.18: 5 residues within 4Å: Chain B: Y.60, L.61, S.62, D.68, G.69 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain B: Q.195, I.218, N.219, D.220 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain B: P.10, Q.11, K.39 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain B: F.8, W.40, P.145 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain A: F.197 Chain B: K.73 Ligand excluded by PLIP

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

EDO.13: 5 residues within 4Å: Chain A: G.49, D.50, K.73, T.74, P.75 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.73

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

PEG.23: 3 residues within 4Å: Chain B: Q.138, W.140, P.141 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.138 Water bridges: B:Q.142, B:Q.142, B:D.143, B:D.143

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
B

B
C

Phosphodiesterase Olei02445

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