SMTL ID : 2vc7.2 (1 other biounit)

Structural basis for natural lactonase and promiscuous phosphotriesterase activities

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

2 x FE2: FE (II) ION(Non-covalent)

FE2.1: 6 residues within 4Å: Chain A: H.22, H.24, K.137, D.256 Ligands: CO.2, HT5.15 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.22, A:H.24, A:D.256, H2O.8 FE2.16: 6 residues within 4Å: Chain B: H.22, H.24, K.137, D.256 Ligands: CO.17, HT5.30 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.22, B:H.24, B:D.256, H2O.15

2 x CO: COBALT (II) ION(Non-covalent)

CO.2: 6 residues within 4Å: Chain A: K.137, H.170, H.199, R.223 Ligands: FE2.1, HT5.15 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.170, A:H.199, H2O.8 CO.17: 5 residues within 4Å: Chain B: K.137, H.170, H.199 Ligands: FE2.16, HT5.30 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.170, B:H.199, H2O.15

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: N.160, K.164, G.189, V.190, D.191, K.194 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.160, A:K.164, A:D.191 Water bridges: A:G.189 GOL.5: 6 residues within 4Å: Chain A: L.5, K.8, D.9, I.11, N.89 Ligands: EDO.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.8, A:N.89 GOL.6: 3 residues within 4Å: Chain A: P.289, K.292, R.293 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.289, A:R.293 GOL.10: 4 residues within 4Å: Chain A: R.77, E.80, K.81, K.84 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.80, A:K.84 GOL.11: 7 residues within 4Å: Chain A: Y.99, D.141, H.170, R.223, F.229, W.263 Ligands: HT5.15 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.99, A:H.170, A:R.223, A:R.223 GOL.13: 2 residues within 4Å: Chain A: D.249, K.311 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.311 GOL.18: 6 residues within 4Å: Chain B: N.160, K.164, G.189, V.190, D.191, K.194 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.160, B:D.191 GOL.21: 5 residues within 4Å: Chain B: F.18, F.59, K.292, E.298, I.301 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.292, B:E.298 GOL.22: 6 residues within 4Å: Chain A: L.102, F.104 Chain B: I.98, Y.99, I.100, D.101 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.99, B:I.100, B:D.101, B:D.101, A:L.102 Water bridges: A:F.104 GOL.25: 7 residues within 4Å: Chain A: Q.34 Chain B: R.26, F.28, R.33, E.42, D.75 Ligands: EDO.26 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.26, B:R.26, B:E.42, B:D.75, A:Q.34

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

EDO.4: 9 residues within 4Å: Chain A: P.4, L.5, K.8, D.9, S.10, L.130, N.131, K.132 Ligands: EDO.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.5, A:L.130, A:N.131, A:K.132 EDO.7: 5 residues within 4Å: Chain A: H.120, E.124, G.125, G.128, T.129 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.128 Water bridges: A:H.120 EDO.8: 2 residues within 4Å: Chain A: H.38 Chain B: H.120 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.120 EDO.9: 5 residues within 4Å: Chain A: M.57, K.62, G.87, N.89 Ligands: GOL.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.62, A:N.89, A:N.89 EDO.12: 5 residues within 4Å: Chain A: M.1, R.2, S.10, K.132 Ligands: EDO.4 No protein-ligand interaction detected (PLIP) EDO.14: 6 residues within 4Å: Chain A: S.171, N.172, A.173, H.174, D.202, F.229 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.172, A:A.173, A:H.199 EDO.19: 9 residues within 4Å: Chain B: P.4, L.5, K.8, D.9, S.10, L.130, N.131, K.132 Ligands: EDO.29 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.5, B:D.9, B:L.130, B:K.132 EDO.20: 6 residues within 4Å: Chain B: A.213, D.214, G.246, Y.247, D.249, K.250 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.213, B:D.249 EDO.23: 8 residues within 4Å: Chain B: S.171, N.172, A.173, H.174, H.199, D.202, F.229 Ligands: EDO.24 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.173, B:H.199, B:D.202, B:R.223 EDO.24: 4 residues within 4Å: Chain B: Y.99, F.229, W.263 Ligands: EDO.23 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.223 EDO.26: 4 residues within 4Å: Chain B: R.33, P.37, Y.40 Ligands: GOL.25 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.33, B:Y.40 EDO.27: 3 residues within 4Å: Chain B: N.48, N.51, E.52 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.51, B:E.52 EDO.28: 3 residues within 4Å: Chain B: E.42, D.43, K.81 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.42, B:K.81 EDO.29: 3 residues within 4Å: Chain B: K.8, N.131 Ligands: EDO.19 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.8, B:K.8, B:N.131

2 x HT5: (4S)-4-(decanoylamino)-5-hydroxy-3,4-dihydro-2H-thiophenium(Non-covalent)

HT5.15: 17 residues within 4Å: Chain A: L.72, Y.97, K.137, H.170, R.223, L.226, F.229, C.258, I.261, W.263, T.265, A.266, K.271, L.274 Ligands: FE2.1, CO.2, GOL.11 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.226, A:L.226, A:F.229, A:I.261, A:A.266, A:K.271, A:L.274, A:L.274 Hydrogen bonds: A:R.223 HT5.30: 21 residues within 4Å: Chain B: H.24, V.27, L.72, Y.97, K.137, H.170, R.223, L.226, L.228, F.229, D.256, C.258, I.261, W.263, T.265, A.266, K.267, K.271, W.278 Ligands: FE2.16, CO.17 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.226, B:L.226, B:L.228, B:F.229, B:I.261, B:K.271, B:W.278 Hydrogen bonds: B:Y.97, B:R.223 Water bridges: B:R.223

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Elias, M. et al., Structural Basis for Natural Lactonase and Promiscuous Phosphotriesterase Activities. J.Mol.Biol. (2008)

Release Date

2008-04-15

Peptides

ARYLDIALKYLPHOSPHATASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

ARYLDIALKYLPHOSPHATASE

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