SMTL ID : 2uui.1

Crystal structure of Human Leukotriene C4 Synthase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-trimer

Ligands

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

NI.1: 8 residues within 4Å: Chain A: H.5, H.7 Chain B: H.5, H.7 Chain C: H.5, H.7 Ligands: NI.22, NI.43 6 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A, 2 interactions with chain B Metal complexes: C:H.5, C:H.7, A:H.5, A:H.7, B:H.5, B:H.7 NI.2: 2 residues within 4Å: Chain A: H.2, H.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.2, A:H.4 NI.3: 3 residues within 4Å: Chain A: H.3, H.4, H.5 No protein-ligand interaction detected (PLIP) NI.22: 8 residues within 4Å: Chain A: H.5, H.7 Chain B: H.5, H.7 Chain C: H.5, H.7 Ligands: NI.1, NI.43 6 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A, 2 interactions with chain B Metal complexes: C:H.5, C:H.7, A:H.5, A:H.7, B:H.5, B:H.7 NI.23: 2 residues within 4Å: Chain B: H.2, H.4 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.2, B:H.4 NI.24: 3 residues within 4Å: Chain B: H.3, H.4, H.5 No protein-ligand interaction detected (PLIP) NI.43: 8 residues within 4Å: Chain A: H.5, H.7 Chain B: H.5, H.7 Chain C: H.5, H.7 Ligands: NI.1, NI.22 6 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A, 2 interactions with chain B Metal complexes: C:H.5, C:H.7, A:H.5, A:H.7, B:H.5, B:H.7 NI.44: 2 residues within 4Å: Chain C: H.2, H.4 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.2, C:H.4 NI.45: 3 residues within 4Å: Chain C: H.3, H.4, H.5 No protein-ligand interaction detected (PLIP)

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

LMT.4: 5 residues within 4Å: Chain A: Y.115, R.119, W.122 Ligands: LMT.5, PLM.10 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.119, A:W.122 Hydrogen bonds: A:R.119 LMT.5: 10 residues within 4Å: Chain A: R.110, L.114, Y.115, W.122 Chain B: L.30, I.33, R.37 Ligands: LMT.4, PLM.10, SO4.15 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.122, A:W.122, B:L.30 Hydrogen bonds: A:R.110, A:Y.115, B:R.37 Water bridges: A:Y.65, A:Y.65, A:Y.65, A:R.110 LMT.25: 5 residues within 4Å: Chain B: Y.115, R.119, W.122 Ligands: LMT.26, PLM.31 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.119, B:W.122 Hydrogen bonds: B:R.119 LMT.26: 10 residues within 4Å: Chain B: R.110, L.114, Y.115, W.122 Chain C: L.30, I.33, R.37 Ligands: LMT.25, PLM.31, SO4.36 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:W.122, B:W.122, C:L.30 Hydrogen bonds: B:R.110, C:R.37 Water bridges: B:Y.65, B:Y.65, B:Y.65, B:R.110 LMT.46: 5 residues within 4Å: Chain C: Y.115, R.119, W.122 Ligands: LMT.47, PLM.52 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:R.119, C:W.122 Hydrogen bonds: C:R.119 LMT.47: 10 residues within 4Å: Chain A: L.30, I.33, R.37 Chain C: R.110, L.114, Y.115, W.122 Ligands: LMT.46, PLM.52, SO4.57 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:W.122, C:W.122, A:L.30 Hydrogen bonds: C:R.110, C:Y.115, A:R.37 Water bridges: C:Y.65, C:Y.65, C:Y.65, C:R.110

42 x PLM: PALMITIC ACID(Non-covalent)(Non-functional Binders)

PLM.6: 4 residues within 4Å: Chain A: Y.27, F.94, R.98, Q.101 Ligand excluded by PLIP PLM.7: 5 residues within 4Å: Chain A: H.135, F.136, A.139 Chain B: L.13 Ligands: PLM.9 Ligand excluded by PLIP PLM.8: 5 residues within 4Å: Chain A: L.20, L.90, F.94, L.97 Ligands: PLM.17 Ligand excluded by PLIP PLM.9: 6 residues within 4Å: Chain A: L.132, F.136 Chain B: L.13, L.19 Ligands: PLM.7, PLM.20 Ligand excluded by PLIP PLM.10: 5 residues within 4Å: Chain A: W.122, V.125, A.129 Ligands: LMT.4, LMT.5 Ligand excluded by PLIP PLM.11: 1 residues within 4Å: Chain A: R.150 Ligand excluded by PLIP PLM.12: 10 residues within 4Å: Chain A: E.10, V.11, W.74, G.77, I.78, E.82 Chain B: W.74 Ligands: PLM.13, PLM.33, PLM.54 Ligand excluded by PLIP PLM.13: 4 residues within 4Å: Chain A: H.81 Chain B: H.6, K.8 Ligands: PLM.12 Ligand excluded by PLIP PLM.16: 4 residues within 4Å: Chain A: F.79, F.80, L.130, A.134 Ligand excluded by PLIP PLM.17: 2 residues within 4Å: Ligands: PLM.8, PLM.60 Ligand excluded by PLIP PLM.18: 1 residues within 4Å: Ligands: PLM.38 Ligand excluded by PLIP PLM.19: 4 residues within 4Å: Chain B: L.13, V.17, G.83, L.90 Ligand excluded by PLIP PLM.20: 1 residues within 4Å: Ligands: PLM.9 Ligand excluded by PLIP PLM.21: 1 residues within 4Å: Chain A: Q.108 Ligand excluded by PLIP PLM.27: 4 residues within 4Å: Chain B: Y.27, F.94, R.98, Q.101 Ligand excluded by PLIP PLM.28: 5 residues within 4Å: Chain B: H.135, F.136, A.139 Chain C: L.13 Ligands: PLM.30 Ligand excluded by PLIP PLM.29: 5 residues within 4Å: Chain B: L.20, L.90, F.94, L.97 Ligands: PLM.38 Ligand excluded by PLIP PLM.30: 6 residues within 4Å: Chain B: L.132, F.136 Chain C: L.13, L.19 Ligands: PLM.28, PLM.41 Ligand excluded by PLIP PLM.31: 5 residues within 4Å: Chain B: W.122, V.125, A.129 Ligands: LMT.25, LMT.26 Ligand excluded by PLIP PLM.32: 1 residues within 4Å: Chain B: R.150 Ligand excluded by PLIP PLM.33: 10 residues within 4Å: Chain B: E.10, V.11, W.74, G.77, I.78, E.82 Chain C: W.74 Ligands: PLM.12, PLM.34, PLM.54 Ligand excluded by PLIP PLM.34: 4 residues within 4Å: Chain B: H.81 Chain C: H.6, K.8 Ligands: PLM.33 Ligand excluded by PLIP PLM.37: 4 residues within 4Å: Chain B: F.79, F.80, L.130, A.134 Ligand excluded by PLIP PLM.38: 2 residues within 4Å: Ligands: PLM.18, PLM.29 Ligand excluded by PLIP PLM.39: 1 residues within 4Å: Ligands: PLM.59 Ligand excluded by PLIP PLM.40: 4 residues within 4Å: Chain C: L.13, V.17, G.83, L.90 Ligand excluded by PLIP PLM.41: 1 residues within 4Å: Ligands: PLM.30 Ligand excluded by PLIP PLM.42: 1 residues within 4Å: Chain B: Q.108 Ligand excluded by PLIP PLM.48: 4 residues within 4Å: Chain C: Y.27, F.94, R.98, Q.101 Ligand excluded by PLIP PLM.49: 5 residues within 4Å: Chain A: L.13 Chain C: H.135, F.136, A.139 Ligands: PLM.51 Ligand excluded by PLIP PLM.50: 5 residues within 4Å: Chain C: L.20, L.90, F.94, L.97 Ligands: PLM.59 Ligand excluded by PLIP PLM.51: 6 residues within 4Å: Chain A: L.13, L.19 Chain C: L.132, F.136 Ligands: PLM.49, PLM.62 Ligand excluded by PLIP PLM.52: 5 residues within 4Å: Chain C: W.122, V.125, A.129 Ligands: LMT.46, LMT.47 Ligand excluded by PLIP PLM.53: 1 residues within 4Å: Chain C: R.150 Ligand excluded by PLIP PLM.54: 10 residues within 4Å: Chain A: W.74 Chain C: E.10, V.11, W.74, G.77, I.78, E.82 Ligands: PLM.12, PLM.33, PLM.55 Ligand excluded by PLIP PLM.55: 4 residues within 4Å: Chain A: H.6, K.8 Chain C: H.81 Ligands: PLM.54 Ligand excluded by PLIP PLM.58: 4 residues within 4Å: Chain C: F.79, F.80, L.130, A.134 Ligand excluded by PLIP PLM.59: 2 residues within 4Å: Ligands: PLM.39, PLM.50 Ligand excluded by PLIP PLM.60: 1 residues within 4Å: Ligands: PLM.17 Ligand excluded by PLIP PLM.61: 4 residues within 4Å: Chain A: L.13, V.17, G.83, L.90 Ligand excluded by PLIP PLM.62: 1 residues within 4Å: Ligands: PLM.51 Ligand excluded by PLIP PLM.63: 1 residues within 4Å: Chain C: Q.108 Ligand excluded by PLIP

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

SO4.14: 4 residues within 4Å: Chain A: R.54, S.106, A.107, Q.108 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.106, A:A.107, A:Q.108 Water bridges: A:R.54 Salt bridges: A:R.54 SO4.15: 6 residues within 4Å: Chain A: N.61, Y.99, Y.103, R.110, L.114 Ligands: LMT.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.61, A:Y.99 Water bridges: A:Y.103, A:R.110, A:R.110 Salt bridges: A:R.110 SO4.35: 4 residues within 4Å: Chain B: R.54, S.106, A.107, Q.108 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.106, B:A.107, B:Q.108 Water bridges: B:R.54 Salt bridges: B:R.54 SO4.36: 6 residues within 4Å: Chain B: N.61, Y.99, Y.103, R.110, L.114 Ligands: LMT.26 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.61, B:Y.99 Water bridges: B:Y.103, B:R.110, B:R.110 Salt bridges: B:R.110 SO4.56: 4 residues within 4Å: Chain C: R.54, S.106, A.107, Q.108 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.106, C:A.107, C:Q.108 Water bridges: C:R.54 Salt bridges: C:R.54 SO4.57: 6 residues within 4Å: Chain C: N.61, Y.99, Y.103, R.110, L.114 Ligands: LMT.47 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.61 Water bridges: C:Y.103, C:R.110, C:R.110 Salt bridges: C:R.110

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martinez Molina, D. et al., Structural Basis for Synthesis of Inflammatory Mediators by Human Leukotriene C4 Synthase. Nature (2007)

Release Date

2007-07-17

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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