SMTL ID : 3o4p.1

DFPase at 0.85 Angstrom resolution (H atoms included)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 0.85 Å

Oligo State

monomer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: L.309, G.312, I.313, F.314 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.313, A:F.314, A:F.314 Water bridges: A:L.309 GOL.2: 1 residues within 4Å: Chain A: D.143 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.144

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.3: 7 residues within 4Å: Chain A: K.43, P.44, N.67, G.68, Y.69, G.70, R.91 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.43, A:G.70 Water bridges: A:R.91, A:R.91 Salt bridges: A:K.43, A:R.91 MES.4: 6 residues within 4Å: Chain A: E.65, V.66, T.102, F.103, E.104, E.105 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.103, A:F.103 Salt bridges: A:E.104

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

EDO.5: 6 residues within 4Å: Chain A: V.167, D.168, Y.203, I.211, E.212 Ligands: MXE.17 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.211 Water bridges: A:D.168 EDO.6: 8 residues within 4Å: Chain A: F.86, F.124, L.130, F.158, T.159, T.160, G.162 Ligands: PEG.19 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.160, A:G.162 EDO.7: 4 residues within 4Å: Chain A: R.115, E.138, P.141, A.142 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.115 EDO.8: 7 residues within 4Å: Chain A: P.196, K.198, T.223, H.224, E.225, G.226 Ligands: PGE.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.198, A:T.223 Water bridges: A:G.226 EDO.9: 5 residues within 4Å: Chain A: H.219, I.220, P.221, Q.258, P.259 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.258 EDO.10: 4 residues within 4Å: Chain A: M.148, Q.149, E.225 Ligands: PGE.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.225, A:E.225 EDO.11: 3 residues within 4Å: Chain A: G.256, G.257, Q.258 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.258 EDO.12: 4 residues within 4Å: Chain A: P.18, E.37, V.38, E.39 No protein-ligand interaction detected (PLIP)

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.13: 9 residues within 4Å: Chain A: M.148, Q.149, Q.172, P.196, T.197, K.198, E.225 Ligands: EDO.8, EDO.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.148 Water bridges: A:Q.172 PGE.14: 4 residues within 4Å: Chain A: T.279, K.280, T.281, E.296 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.280, A:K.280, A:T.281

2 x DXE: 1,2-DIMETHOXYETHANE(Non-covalent)

DXE.15: 3 residues within 4Å: Chain A: W.244, K.269, H.287 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.269 DXE.16: 7 residues within 4Å: Chain A: P.8, L.9, K.280, F.295, E.296, W.297, Q.298 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.9

2 x MXE: 2-METHOXYETHANOL(Non-covalent)

MXE.17: 5 residues within 4Å: Chain A: Y.203, E.212, N.213, K.214 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.213, A:K.214 MXE.18: 9 residues within 4Å: Chain A: K.151, T.169, A.170, F.171, Q.172, E.194, T.197, W.201, K.214 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.151, A:K.214 Water bridges: A:D.168, A:T.169

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

PEG.19: 5 residues within 4Å: Chain A: Q.84, F.86, I.106, F.158 Ligands: EDO.6 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.79, A:Q.84, A:Q.84 PEG.20: 4 residues within 4Å: Chain A: K.63, P.64, E.65, F.103 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.63, A:E.65, A:E.65 Water bridges: A:K.63

1 x ME2: 1-ETHOXY-2-(2-METHOXYETHOXY)ETHANE(Non-covalent)

ME2.21: 5 residues within 4Å: Chain A: V.5, I.6, H.248, R.262, R.264 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.264 Water bridges: A:R.262

2 x CA: CALCIUM ION(Non-covalent)

CA.22: 6 residues within 4Å: Chain A: E.21, N.120, D.121, N.175, D.229, N.272 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.21, A:D.229, H2O.1, H2O.1, H2O.4 CA.23: 4 residues within 4Å: Chain A: P.23, D.232, L.273, H.274 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.232, A:L.273, A:H.274, H2O.1, H2O.5, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Elias, M. et al., Hydrogen atoms in protein structures: high-resolution X-ray diffraction structure of the DFPase. BMC Res Notes (2013)

Release Date

2011-08-17

Peptides

Diisopropyl-fluorophosphatase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Diisopropyl-fluorophosphatase

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