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

Structure of human Leukotriene C4 synthase mutant R31Q in complex with glutathione

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-trimer

Ligands

6 x PAM: PALMITOLEIC ACID(Non-covalent)

PAM.1: 7 residues within 4Å: Chain A: E.9, W.73, I.77 Chain C: L.69, W.73 Ligands: PAM.16, PAM.31 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:W.73, A:I.77, A:I.77, C:L.69, C:W.73, C:W.73 Water bridges: C:K.7 PAM.15: 8 residues within 4Å: Chain A: L.12, A.15, V.16, L.19, G.82, L.86, L.89 Ligands: PLM.18 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.15, A:V.16, A:L.19, A:L.86, A:L.86, A:L.89 PAM.16: 7 residues within 4Å: Chain A: L.69, W.73 Chain B: E.9, W.73, I.77 Ligands: PAM.1, PAM.31 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:W.73, B:I.77, B:I.77, A:L.69, A:W.73, A:W.73 Water bridges: A:K.7 PAM.30: 8 residues within 4Å: Chain B: L.12, A.15, V.16, L.19, G.82, L.86, L.89 Ligands: PLM.33 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.15, B:V.16, B:L.19, B:L.86, B:L.86, B:L.89 PAM.31: 7 residues within 4Å: Chain B: L.69, W.73 Chain C: E.9, W.73, I.77 Ligands: PAM.1, PAM.16 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:L.69, B:W.73, B:W.73, C:W.73, C:I.77, C:I.77 Water bridges: B:K.7 PAM.45: 8 residues within 4Å: Chain C: L.12, A.15, V.16, L.19, G.82, L.86, L.89 Ligands: PLM.3 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:A.15, C:V.16, C:L.19, C:L.86, C:L.86, C:L.89

18 x PLM: PALMITIC ACID(Non-covalent)

PLM.2: 3 residues within 4Å: Chain A: P.137, L.140, R.141 Ligand excluded by PLIP PLM.3: 5 residues within 4Å: Chain A: L.131, F.135 Chain C: L.12 Ligands: PLM.6, PAM.45 Ligand excluded by PLIP PLM.4: 3 residues within 4Å: Chain A: L.23, Y.26, Q.100 Ligand excluded by PLIP PLM.6: 2 residues within 4Å: Chain A: A.139 Ligands: PLM.3 Ligand excluded by PLIP PLM.7: 2 residues within 4Å: Chain A: W.121, A.125 Ligand excluded by PLIP PLM.8: 4 residues within 4Å: Chain A: L.19, L.89, F.93, L.96 Ligand excluded by PLIP PLM.17: 3 residues within 4Å: Chain B: P.137, L.140, R.141 Ligand excluded by PLIP PLM.18: 5 residues within 4Å: Chain A: L.12 Chain B: L.131, F.135 Ligands: PAM.15, PLM.21 Ligand excluded by PLIP PLM.19: 3 residues within 4Å: Chain B: L.23, Y.26, Q.100 Ligand excluded by PLIP PLM.21: 2 residues within 4Å: Chain B: A.139 Ligands: PLM.18 Ligand excluded by PLIP PLM.22: 2 residues within 4Å: Chain B: W.121, A.125 Ligand excluded by PLIP PLM.23: 4 residues within 4Å: Chain B: L.19, L.89, F.93, L.96 Ligand excluded by PLIP PLM.32: 3 residues within 4Å: Chain C: P.137, L.140, R.141 Ligand excluded by PLIP PLM.33: 5 residues within 4Å: Chain B: L.12 Chain C: L.131, F.135 Ligands: PAM.30, PLM.36 Ligand excluded by PLIP PLM.34: 3 residues within 4Å: Chain C: L.23, Y.26, Q.100 Ligand excluded by PLIP PLM.36: 2 residues within 4Å: Chain C: A.139 Ligands: PLM.33 Ligand excluded by PLIP PLM.37: 2 residues within 4Å: Chain C: W.121, A.125 Ligand excluded by PLIP PLM.38: 4 residues within 4Å: Chain C: L.19, L.89, F.93, L.96 Ligand excluded by PLIP

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 3 residues within 4Å: Chain A: S.105, A.106, Q.107 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.105, A:A.106, A:Q.107 Water bridges: A:R.53 SO4.9: 1 residues within 4Å: Chain A: R.39 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.39 SO4.20: 3 residues within 4Å: Chain B: S.105, A.106, Q.107 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.105, B:A.106, B:Q.107 Water bridges: B:R.53 SO4.24: 1 residues within 4Å: Chain B: R.39 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.39 SO4.35: 3 residues within 4Å: Chain C: S.105, A.106, Q.107 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.105, C:A.106, C:Q.107 Water bridges: C:R.53 SO4.39: 1 residues within 4Å: Chain C: R.39 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.39

6 x NI: NICKEL (II) ION(Non-covalent)

NI.10: 8 residues within 4Å: Chain A: H.4, H.6 Chain B: H.4, H.6 Chain C: H.4, H.6 Ligands: NI.25, NI.40 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 1 interactions with chain A Metal complexes: B:H.4, B:H.6, C:H.4, C:H.6, A:H.6 NI.11: 2 residues within 4Å: Chain A: H.1, H.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.1, A:H.3 NI.25: 8 residues within 4Å: Chain A: H.4, H.6 Chain B: H.4, H.6 Chain C: H.4, H.6 Ligands: NI.10, NI.40 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 interactions with chain C Metal complexes: B:H.6, A:H.4, A:H.6, C:H.4, C:H.6 NI.26: 2 residues within 4Å: Chain B: H.1, H.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.1, B:H.3 NI.40: 8 residues within 4Å: Chain A: H.4, H.6 Chain B: H.4, H.6 Chain C: H.4, H.6 Ligands: NI.10, NI.25 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A, 2 interactions with chain B Metal complexes: C:H.6, A:H.4, A:H.6, B:H.4, B:H.6 NI.41: 2 residues within 4Å: Chain C: H.1, H.3 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.1, C:H.3

3 x GSH: GLUTATHIONE(Non-covalent)

GSH.12: 16 residues within 4Å: Chain A: R.56, N.60, E.63, Y.64, Y.98, Y.102, R.109, L.113 Chain C: S.28, V.31, I.32, R.35, P.42, Y.55, Q.58 Ligands: LMT.13 12 PLIP interactions: 7 interactions with chain A, 5 interactions with chain C Hydrogen bonds: A:R.56, A:E.63, A:Y.98, A:Y.102, A:Y.102, C:Q.58 Salt bridges: A:R.56, A:R.56, C:R.35, C:R.35 Hydrophobic interactions: C:V.31, C:I.32 GSH.27: 16 residues within 4Å: Chain A: S.28, V.31, I.32, R.35, P.42, Y.55, Q.58 Chain B: R.56, N.60, E.63, Y.64, Y.98, Y.102, R.109, L.113 Ligands: LMT.28 12 PLIP interactions: 7 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:R.56, B:E.63, B:Y.98, B:Y.102, B:Y.102, A:Q.58 Salt bridges: B:R.56, B:R.56, A:R.35, A:R.35 Hydrophobic interactions: A:V.31, A:I.32 GSH.42: 16 residues within 4Å: Chain B: S.28, V.31, I.32, R.35, P.42, Y.55, Q.58 Chain C: R.56, N.60, E.63, Y.64, Y.98, Y.102, R.109, L.113 Ligands: LMT.43 12 PLIP interactions: 5 interactions with chain B, 7 interactions with chain C Hydrophobic interactions: B:V.31, B:I.32 Hydrogen bonds: B:Q.58, C:R.56, C:E.63, C:Y.64, C:Y.102, C:Y.102 Salt bridges: B:R.35, B:R.35, C:R.56, C:R.56

3 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.13: 18 residues within 4Å: Chain A: Y.64, A.106, Q.107, R.109, L.110, L.113, Y.114, A.117, L.120, W.121 Chain C: A.25, L.29, I.32, R.35, Q.36, S.41, P.42 Ligands: GSH.12 19 PLIP interactions: 13 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:Y.64, A:L.113, A:Y.114, A:Y.114, A:A.117, A:L.120, A:L.120, A:W.121, A:W.121, C:A.25, C:L.29 Hydrogen bonds: A:R.109, C:I.32, C:Q.36, C:Q.36, C:P.42 Water bridges: A:Q.107, A:Q.107 Salt bridges: A:R.109 LMT.28: 18 residues within 4Å: Chain A: A.25, L.29, I.32, R.35, Q.36, S.41, P.42 Chain B: Y.64, A.106, Q.107, R.109, L.110, L.113, Y.114, A.117, L.120, W.121 Ligands: GSH.27 20 PLIP interactions: 6 interactions with chain A, 14 interactions with chain B Hydrophobic interactions: A:A.25, A:L.29, B:Y.64, B:L.113, B:Y.114, B:Y.114, B:A.117, B:L.120, B:L.120, B:W.121, B:W.121 Hydrogen bonds: A:I.32, A:Q.36, A:Q.36, A:P.42, B:R.109, B:Y.114 Water bridges: B:Q.107, B:Q.107 Salt bridges: B:R.109 LMT.43: 18 residues within 4Å: Chain B: A.25, L.29, I.32, R.35, Q.36, S.41, P.42 Chain C: Y.64, A.106, Q.107, R.109, L.110, L.113, Y.114, A.117, L.120, W.121 Ligands: GSH.42 20 PLIP interactions: 14 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:Y.64, C:L.113, C:Y.114, C:Y.114, C:A.117, C:L.120, C:L.120, C:W.121, C:W.121, B:A.25, B:L.29 Hydrogen bonds: C:R.109, C:Y.114, B:I.32, B:Q.36, B:Q.36, B:P.42 Water bridges: C:Q.107, C:Q.107 Salt bridges: C:R.109

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 2 residues within 4Å: Chain A: Y.114, R.118 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.118 GOL.29: 2 residues within 4Å: Chain B: Y.114, R.118 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.118 GOL.44: 2 residues within 4Å: Chain C: Y.114, R.118 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rinaldo-Matthis, A. et al., Arginine 104 is a key catalytic residue in leukotriene C4 synthase. J.Biol.Chem. (2010)

Release Date

2010-10-27

Peptides

Leukotriene C4 synthase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Membrane

We predict this structure to be a membrane protein.
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Leukotriene C4 synthase

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