SMTL ID : 3pcv.1

Crystal structure analysis of human leukotriene C4 synthase at 1.9 angstrom resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

3 x GSH: GLUTATHIONE(Non-covalent)

GSH.1: 16 residues within 4Å: Chain A: R.51, N.55, E.58, Y.59, Y.93, Y.97, R.104, L.108 Chain C: S.23, V.26, I.27, R.30, P.37, Y.50, Q.53 Ligands: EDO.60 13 PLIP interactions: 5 interactions with chain C, 8 interactions with chain A Hydrophobic interactions: C:V.26, C:I.27 Hydrogen bonds: C:Q.53, A:R.51, A:N.55, A:E.58, A:Y.93, A:Y.97, A:Y.97 Salt bridges: C:R.30, C:R.30, A:R.51, A:R.51 GSH.23: 16 residues within 4Å: Chain A: S.23, V.26, I.27, R.30, P.37, Y.50, Q.53 Chain B: R.51, N.55, E.58, Y.59, Y.93, Y.97, R.104, L.108 Ligands: EDO.16 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:R.51, B:N.55, B:E.58, B:Y.93, B:Y.97, B:Y.97, A:Q.53 Salt bridges: B:R.51, B:R.51, A:R.30, A:R.30 Hydrophobic interactions: A:V.26, A:I.27 GSH.45: 16 residues within 4Å: Chain B: S.23, V.26, I.27, R.30, P.37, Y.50, Q.53 Chain C: R.51, N.55, E.58, Y.59, Y.93, Y.97, R.104, L.108 Ligands: EDO.38 13 PLIP interactions: 8 interactions with chain C, 5 interactions with chain B Hydrogen bonds: C:R.51, C:N.55, C:E.58, C:Y.59, C:Y.97, C:Y.97, B:Q.53 Salt bridges: C:R.51, C:R.51, B:R.30, B:R.30 Hydrophobic interactions: B:V.26, B:I.27

33 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)(Non-functional Binders)

LMT.2: 7 residues within 4Å: Chain A: L.7, A.10 Chain B: A.123, L.127, F.130 Ligands: LMT.6, LMT.33 Ligand excluded by PLIP LMT.3: 6 residues within 4Å: Chain A: A.20 Chain B: Y.59, L.115, W.116, V.119 Ligands: EDO.16 Ligand excluded by PLIP LMT.4: 3 residues within 4Å: Chain A: L.14, Y.21, Q.95 Ligand excluded by PLIP LMT.5: 4 residues within 4Å: Chain A: F.73, F.74, L.124, A.128 Ligand excluded by PLIP LMT.6: 7 residues within 4Å: Chain A: A.10, L.14, G.77, A.80, L.81, L.84 Ligands: LMT.2 Ligand excluded by PLIP LMT.7: 6 residues within 4Å: Chain A: W.68, I.72 Chain C: M.1, W.68 Ligands: LMT.29, LMT.51 Ligand excluded by PLIP LMT.8: 5 residues within 4Å: Chain A: W.116, L.117, A.120, A.123 Chain C: L.17 Ligand excluded by PLIP LMT.9: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LMT.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LMT.11: 2 residues within 4Å: Chain A: L.127 Ligands: LMT.46 Ligand excluded by PLIP LMT.12: 2 residues within 4Å: Chain A: L.14, L.91 Ligand excluded by PLIP LMT.24: 7 residues within 4Å: Chain B: L.7, A.10 Chain C: A.123, L.127, F.130 Ligands: LMT.28, LMT.55 Ligand excluded by PLIP LMT.25: 6 residues within 4Å: Chain B: A.20 Chain C: Y.59, L.115, W.116, V.119 Ligands: EDO.38 Ligand excluded by PLIP LMT.26: 3 residues within 4Å: Chain B: L.14, Y.21, Q.95 Ligand excluded by PLIP LMT.27: 4 residues within 4Å: Chain B: F.73, F.74, L.124, A.128 Ligand excluded by PLIP LMT.28: 7 residues within 4Å: Chain B: A.10, L.14, G.77, A.80, L.81, L.84 Ligands: LMT.24 Ligand excluded by PLIP LMT.29: 6 residues within 4Å: Chain A: M.1, W.68 Chain B: W.68, I.72 Ligands: LMT.7, LMT.51 Ligand excluded by PLIP LMT.30: 5 residues within 4Å: Chain A: L.17 Chain B: W.116, L.117, A.120, A.123 Ligand excluded by PLIP LMT.31: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LMT.32: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LMT.33: 2 residues within 4Å: Chain B: L.127 Ligands: LMT.2 Ligand excluded by PLIP LMT.34: 2 residues within 4Å: Chain B: L.14, L.91 Ligand excluded by PLIP LMT.46: 7 residues within 4Å: Chain A: A.123, L.127, F.130 Chain C: L.7, A.10 Ligands: LMT.11, LMT.50 Ligand excluded by PLIP LMT.47: 6 residues within 4Å: Chain A: Y.59, L.115, W.116, V.119 Chain C: A.20 Ligands: EDO.60 Ligand excluded by PLIP LMT.48: 3 residues within 4Å: Chain C: L.14, Y.21, Q.95 Ligand excluded by PLIP LMT.49: 4 residues within 4Å: Chain C: F.73, F.74, L.124, A.128 Ligand excluded by PLIP LMT.50: 7 residues within 4Å: Chain C: A.10, L.14, G.77, A.80, L.81, L.84 Ligands: LMT.46 Ligand excluded by PLIP LMT.51: 6 residues within 4Å: Chain B: M.1, W.68 Chain C: W.68, I.72 Ligands: LMT.7, LMT.29 Ligand excluded by PLIP LMT.52: 5 residues within 4Å: Chain B: L.17 Chain C: W.116, L.117, A.120, A.123 Ligand excluded by PLIP LMT.53: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LMT.54: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LMT.55: 2 residues within 4Å: Chain C: L.127 Ligands: LMT.24 Ligand excluded by PLIP LMT.56: 2 residues within 4Å: Chain C: L.14, L.91 Ligand excluded by PLIP

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

EDO.13: 6 residues within 4Å: Chain A: Y.50, R.51 Chain C: T.40, Y.50 Ligands: EDO.35, EDO.57 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:Y.50, A:Y.50, A:R.51, C:T.40, C:T.40 EDO.14: 7 residues within 4Å: Chain A: E.58, Y.59, L.62 Chain C: Q.19, S.23, Q.53, S.57 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Q.19, C:S.23, C:Q.53, A:E.58 EDO.15: 3 residues within 4Å: Chain A: R.104 Chain C: P.37 Ligands: EDO.60 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.104, A:R.104 EDO.16: 6 residues within 4Å: Chain A: I.27 Chain B: R.104, L.105 Ligands: LMT.3, GSH.23, EDO.37 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.104 EDO.35: 6 residues within 4Å: Chain A: T.40, Y.50 Chain B: Y.50, R.51 Ligands: EDO.13, EDO.57 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Y.50, B:Y.50, B:R.51, A:T.40, A:T.40, A:Y.50 EDO.36: 7 residues within 4Å: Chain A: Q.19, S.23, Q.53, S.57 Chain B: E.58, Y.59, L.62 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:E.58, A:Q.19, A:S.23, A:Q.53 EDO.37: 3 residues within 4Å: Chain A: P.37 Chain B: R.104 Ligands: EDO.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.104, B:R.104 EDO.38: 6 residues within 4Å: Chain B: I.27 Chain C: R.104, L.105 Ligands: LMT.25, GSH.45, EDO.59 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.104 EDO.57: 6 residues within 4Å: Chain B: T.40, Y.50 Chain C: Y.50, R.51 Ligands: EDO.13, EDO.35 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:T.40, B:T.40, B:Y.50, C:Y.50, C:R.51 EDO.58: 7 residues within 4Å: Chain B: Q.19, S.23, Q.53, S.57 Chain C: E.58, Y.59, L.62 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Q.19, B:S.23, B:Q.53, C:E.58 EDO.59: 3 residues within 4Å: Chain B: P.37 Chain C: R.104 Ligands: EDO.38 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.104, C:R.104 EDO.60: 6 residues within 4Å: Chain A: R.104, L.105 Chain C: I.27 Ligands: GSH.1, EDO.15, LMT.47 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.104

12 x UNL: UNKNOWN LIGAND(Non-functional Binders)

UNL.17: 1 residues within 4Å: Chain A: L.117 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.117 UNL.18: 1 residues within 4Å: Chain B: W.116 No protein-ligand interaction detected (PLIP) UNL.19: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) UNL.20: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) UNL.39: 1 residues within 4Å: Chain B: L.117 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.117 UNL.40: 1 residues within 4Å: Chain C: W.116 No protein-ligand interaction detected (PLIP) UNL.41: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) UNL.42: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) UNL.61: 1 residues within 4Å: Chain C: L.117 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.117 UNL.62: 1 residues within 4Å: Chain A: W.116 No protein-ligand interaction detected (PLIP) UNL.63: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) UNL.64: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

SO4.21: 4 residues within 4Å: Chain A: R.48, S.100, A.101, Q.102 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.101, A:Q.102 Water bridges: A:R.48, A:R.48 Salt bridges: A:R.48 SO4.22: 1 residues within 4Å: Chain A: R.34 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.34 SO4.43: 4 residues within 4Å: Chain B: R.48, S.100, A.101, Q.102 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.101, B:Q.102 Water bridges: B:R.48, B:R.48 Salt bridges: B:R.48 SO4.44: 1 residues within 4Å: Chain B: R.34 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.34 SO4.65: 4 residues within 4Å: Chain C: R.48, S.100, A.101, Q.102 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:A.101, C:Q.102 Water bridges: C:R.48, C:R.48 Salt bridges: C:R.48 SO4.66: 1 residues within 4Å: Chain C: R.34 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.34

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saino, H. et al., The catalytic architecture of leukotriene C4 synthase with two arginine residues. J.Biol.Chem. (2011)

Release Date

2011-03-16

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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