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

Crystal Structure Analysis of neutral ceramidase from Pseudomonas aeruginosa

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.97, H.204, E.411, Y.448 Ligands: GOL.10 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.97, A:H.204, A:E.411, A:Y.448, H2O.297 ZN.24: 5 residues within 4Å: Chain B: H.97, H.204, E.411, Y.448 Ligands: GOL.33 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.97, B:H.204, B:E.411, B:Y.448, H2O.950

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: H.37, D.579, N.580, D.581, T.584 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.37, A:D.581, A:T.584, A:T.584, H2O.42 MG.25: 5 residues within 4Å: Chain B: H.37, D.579, N.580, D.581, T.584 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.37, B:D.581, B:T.584, B:T.584, H2O.695

6 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 6 residues within 4Å: Chain A: F.67, Q.68, S.106, Y.108, A.444, Y.445 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.68, A:Y.445, A:Y.445 Water bridges: A:H.107 FMT.4: 9 residues within 4Å: Chain A: R.43, N.60, D.62, T.96, K.220, G.221, S.224, A.240, F.241 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.43, A:N.60, A:K.220, A:S.224, A:F.241 FMT.5: 5 residues within 4Å: Chain A: T.510, G.511, V.512 Chain B: D.500, S.502 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:C.503 Hydrogen bonds: A:G.511 FMT.26: 6 residues within 4Å: Chain B: F.67, Q.68, S.106, Y.108, A.444, Y.445 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.68, B:Y.445, B:Y.445 Water bridges: B:H.107 FMT.27: 9 residues within 4Å: Chain B: R.43, N.60, D.62, T.96, K.220, G.221, S.224, A.240, F.241 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.43, B:N.60, B:K.220, B:S.224, B:F.241 FMT.28: 5 residues within 4Å: Chain A: D.500, S.502 Chain B: T.510, G.511, V.512 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.511 Water bridges: A:C.503

2 x PLM: PALMITIC ACID(Non-covalent)

PLM.6: 5 residues within 4Å: Chain A: R.298, L.490, P.491, V.492, E.493 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.491, A:E.493 Hydrogen bonds: A:L.490, A:L.490 Water bridges: A:R.298, A:R.298 Salt bridges: A:R.298 PLM.29: 5 residues within 4Å: Chain B: R.298, L.490, P.491, V.492, E.493 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:P.491, B:E.493 Hydrogen bonds: B:L.490, B:L.490 Water bridges: B:R.298, B:R.298 Salt bridges: B:R.298

34 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: D.2, L.3, A.50, A.51 Ligand excluded by PLIP GOL.8: 3 residues within 4Å: Chain A: R.6, E.48, L.141 Ligand excluded by PLIP GOL.9: 7 residues within 4Å: Chain A: H.107, A.109, F.351, Y.386, C.504, Q.505, M.506 Ligand excluded by PLIP GOL.10: 7 residues within 4Å: Chain A: M.24, G.25, H.99, Y.445, Y.448, Y.460 Ligands: ZN.1 Ligand excluded by PLIP GOL.11: 5 residues within 4Å: Chain A: E.152, L.153, R.154, N.155, K.279 Ligand excluded by PLIP GOL.12: 3 residues within 4Å: Chain A: T.206, S.250, P.251 Ligand excluded by PLIP GOL.13: 6 residues within 4Å: Chain A: H.37, F.266, W.582, D.583, Q.585, S.603 Ligand excluded by PLIP GOL.14: 6 residues within 4Å: Chain A: G.84, V.85, Y.86, D.87, N.89, N.90 Ligand excluded by PLIP GOL.15: 2 residues within 4Å: Chain A: S.27 Ligands: GOL.18 Ligand excluded by PLIP GOL.16: 7 residues within 4Å: Chain A: Y.222, Y.225, D.230, R.270, W.582, D.583, P.605 Ligand excluded by PLIP GOL.17: 4 residues within 4Å: Chain A: Y.614, R.616, G.634, S.635 Ligand excluded by PLIP GOL.18: 3 residues within 4Å: Chain A: E.345, L.358 Ligands: GOL.15 Ligand excluded by PLIP GOL.19: 4 residues within 4Å: Chain A: K.32, A.34, H.213, R.587 Ligand excluded by PLIP GOL.20: 1 residues within 4Å: Chain A: L.166 Ligand excluded by PLIP GOL.21: 4 residues within 4Å: Chain A: N.155, N.252, L.253, L.255 Ligand excluded by PLIP GOL.22: 4 residues within 4Å: Chain A: G.192, E.193, L.194, A.284 Ligand excluded by PLIP GOL.23: 3 residues within 4Å: Chain A: E.20, K.32, Q.509 Ligand excluded by PLIP GOL.30: 4 residues within 4Å: Chain B: D.2, L.3, A.50, A.51 Ligand excluded by PLIP GOL.31: 3 residues within 4Å: Chain B: R.6, E.48, L.141 Ligand excluded by PLIP GOL.32: 7 residues within 4Å: Chain B: H.107, A.109, F.351, Y.386, C.504, Q.505, M.506 Ligand excluded by PLIP GOL.33: 7 residues within 4Å: Chain B: M.24, G.25, H.99, Y.445, Y.448, Y.460 Ligands: ZN.24 Ligand excluded by PLIP GOL.34: 5 residues within 4Å: Chain B: E.152, L.153, R.154, N.155, K.279 Ligand excluded by PLIP GOL.35: 3 residues within 4Å: Chain B: T.206, S.250, P.251 Ligand excluded by PLIP GOL.36: 6 residues within 4Å: Chain B: H.37, F.266, W.582, D.583, Q.585, S.603 Ligand excluded by PLIP GOL.37: 6 residues within 4Å: Chain B: G.84, V.85, Y.86, D.87, N.89, N.90 Ligand excluded by PLIP GOL.38: 2 residues within 4Å: Chain B: S.27 Ligands: GOL.41 Ligand excluded by PLIP GOL.39: 7 residues within 4Å: Chain B: Y.222, Y.225, D.230, R.270, W.582, D.583, P.605 Ligand excluded by PLIP GOL.40: 4 residues within 4Å: Chain B: Y.614, R.616, G.634, S.635 Ligand excluded by PLIP GOL.41: 3 residues within 4Å: Chain B: E.345, L.358 Ligands: GOL.38 Ligand excluded by PLIP GOL.42: 4 residues within 4Å: Chain B: K.32, A.34, H.213, R.587 Ligand excluded by PLIP GOL.43: 1 residues within 4Å: Chain B: L.166 Ligand excluded by PLIP GOL.44: 4 residues within 4Å: Chain B: N.155, N.252, L.253, L.255 Ligand excluded by PLIP GOL.45: 4 residues within 4Å: Chain B: G.192, E.193, L.194, A.284 Ligand excluded by PLIP GOL.46: 3 residues within 4Å: Chain B: E.20, K.32, Q.509 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Inoue, T. et al., Mechanistic insights into the hydrolysis and synthesis of ceramide by neutral ceramidase. J.Biol.Chem. (2009)

Release Date

2009-03-03

Peptides

Neutral ceramidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Neutral ceramidase

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