SMTL ID : 3a70.1

Crystal structure of Pseudomonas sp. MIS38 lipase in complex with diethyl phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

22 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: E.253, D.275, D.283, N.284 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.253, A:D.275, A:D.283, H2O.3, H2O.16 CA.2: 4 residues within 4Å: Chain A: K.278, A.281, D.283, D.337 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:K.278, A:A.281, A:D.283, H2O.2, H2O.16 CA.3: 6 residues within 4Å: Chain A: S.374, S.376, D.378, G.391, A.393, D.396 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:S.374, A:S.376, A:D.378, A:G.391, A:A.393 CA.4: 6 residues within 4Å: Chain A: G.383, G.385, D.387, D.400, G.402, N.405 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:G.383, A:G.385, A:D.387, A:D.400, A:G.402 CA.5: 8 residues within 4Å: Chain A: R.392, A.393, G.394, D.396, G.409, G.410, A.411, N.414 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:R.392, A:G.394, A:D.396, A:G.409, A:A.411 CA.6: 7 residues within 4Å: Chain A: T.494, G.496, D.498, G.511, L.512, D.513, D.516 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.494, A:G.496, A:D.498, A:D.513, A:D.516 CA.7: 8 residues within 4Å: Chain A: L.512, D.513, G.514, D.516, G.529, G.530, A.531, D.534 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:L.512, A:G.514, A:D.516, A:G.529, A:D.534 CA.8: 6 residues within 4Å: Chain A: G.521, G.523, D.525, S.538, G.540, D.543 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:G.521, A:G.523, A:D.525, A:S.538, A:G.540 CA.9: 6 residues within 4Å: Chain A: G.530, A.531, G.532, D.534, F.551, D.554 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.530, A:G.532, A:D.534, A:F.551, A:D.554, H2O.7 CA.10: 4 residues within 4Å: Chain A: G.541, T.560, N.562, D.563 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.541, A:T.560, A:D.563, H2O.1, H2O.8 CA.11: 5 residues within 4Å: Chain A: T.118, Q.120, S.144, D.153, D.157 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.118, A:S.144, A:D.153, A:D.157, H2O.6 CA.15: 4 residues within 4Å: Chain B: E.253, D.275, D.283, N.284 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.253, B:D.275, B:D.283, H2O.36, H2O.36 CA.16: 4 residues within 4Å: Chain B: K.278, A.281, D.283, D.337 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:K.278, B:A.281, B:D.283, H2O.39, H2O.40 CA.17: 6 residues within 4Å: Chain B: S.374, S.376, D.378, G.391, A.393, D.396 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:S.374, B:S.376, B:D.378, B:G.391, B:A.393 CA.18: 6 residues within 4Å: Chain B: G.383, G.385, D.387, D.400, G.402, N.405 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:G.383, B:G.385, B:D.387, B:D.400, B:G.402 CA.19: 8 residues within 4Å: Chain B: R.392, A.393, G.394, D.396, G.409, G.410, A.411, N.414 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:R.392, B:G.394, B:D.396, B:G.409, B:A.411 CA.20: 7 residues within 4Å: Chain B: T.494, G.496, D.498, G.511, L.512, D.513, D.516 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:G.496, B:D.498, B:G.511, B:D.513, B:D.516 CA.21: 8 residues within 4Å: Chain B: L.512, D.513, G.514, D.516, G.529, G.530, A.531, D.534 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:L.512, B:G.514, B:D.516, B:G.529, B:D.534 CA.22: 6 residues within 4Å: Chain B: G.521, G.523, D.525, S.538, G.540, D.543 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:G.521, B:G.523, B:D.525, B:S.538, B:G.540 CA.23: 5 residues within 4Å: Chain B: G.530, G.532, D.534, F.551, D.554 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:G.530, B:G.532, B:D.534, B:F.551, B:D.554, H2O.26 CA.24: 4 residues within 4Å: Chain B: G.541, T.560, N.562, D.563 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:G.541, B:T.560, B:D.563, B:D.563, H2O.31 CA.25: 5 residues within 4Å: Chain B: T.118, Q.120, S.144, D.153, D.157 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.118, B:S.144, B:D.153, B:D.157, H2O.26

2 x DEP: DIETHYL PHOSPHONATE(Covalent)

DEP.12: 10 residues within 4Å: Chain A: Y.29, G.142, T.143, D.161, S.207, L.208, V.257, W.310, H.313 Ligands: NPO.13 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.143, A:T.143, A:L.208 Salt bridges: A:H.313 DEP.26: 10 residues within 4Å: Chain B: Y.29, G.142, T.143, D.161, S.207, L.208, V.257, W.310, H.313 Ligands: NPO.27 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.143, B:T.143, B:L.208 Salt bridges: B:H.313

2 x NPO: P-NITROPHENOL(Non-covalent)

NPO.13: 7 residues within 4Å: Chain A: Y.29, L.32, D.33, F.36, A.56, V.66 Ligands: DEP.12 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.32, A:D.33, A:F.36 NPO.27: 5 residues within 4Å: Chain B: L.32, D.33, A.56, V.66 Ligands: DEP.26 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:D.33 Hydrogen bonds: B:A.56 Water bridges: B:F.36

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.14: 1 residues within 4Å: Chain A: N.548 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.548 ACT.28: 2 residues within 4Å: Chain B: V.406, N.548 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.406 Hydrogen bonds: B:N.548, B:N.548

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Angkawidjaja, C. et al., X-ray Crystallographic and MD Simulation Studies on the Mechanism of Interfacial Activation of a Family I.3 Lipase with Two Lids. J.Mol.Biol. (2010)

Release Date

2010-05-26

Peptides

Lipase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Lipase

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