SMTL ID : 3b29.1

Human leukotriene C4 synthase in complex with dodecyl-beta-D-selenomaltoside

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-trimer

Ligands

3 x GSH: GLUTATHIONE(Non-covalent)

GSH.1: 15 residues within 4Å: Chain A: R.51, N.55, E.58, Y.59, Y.93, Y.97, R.104, L.108 Chain B: V.26, I.27, R.30, P.37, Y.50, Q.53 Ligands: LSM.7 12 PLIP interactions: 4 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:V.26, B:I.27 Salt bridges: B:R.30, B:R.30, A:R.51, A:R.51 Hydrogen bonds: A:R.51, A:N.55, A:E.58, A:Y.93, A:Y.97, A:Y.97 GSH.8: 15 residues within 4Å: Chain B: R.51, N.55, E.58, Y.59, Y.93, Y.97, R.104, L.108 Chain C: V.26, I.27, R.30, P.37, Y.50, Q.53 Ligands: LSM.14 12 PLIP interactions: 8 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:R.51, B:N.55, B:E.58, B:Y.93, B:Y.97, B:Y.97 Salt bridges: B:R.51, B:R.51, C:R.30, C:R.30 Hydrophobic interactions: C:V.26, C:I.27 GSH.15: 15 residues within 4Å: Chain A: 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: LSM.21 11 PLIP interactions: 7 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:R.51, C:N.55, C:E.58, C:Y.97, C:Y.97 Salt bridges: C:R.51, C:R.51, A:R.30, A:R.30 Hydrophobic interactions: A:V.26, A:I.27

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

SO4.2: 3 residues within 4Å: Chain A: S.100, A.101, Q.102 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.100, A:A.101, A:Q.102 SO4.9: 3 residues within 4Å: Chain B: S.100, A.101, Q.102 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.100, B:A.101, B:Q.102 SO4.16: 3 residues within 4Å: Chain C: S.100, A.101, Q.102 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.100, C:A.101, C:Q.102

15 x LSM: dodecyl 4-O-alpha-D-glucopyranosyl-1-seleno-beta-D-glucopyranoside(Non-covalent)

LSM.3: 4 residues within 4Å: Chain A: W.68 Chain C: I.72 Ligands: LSM.10, LSM.17 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:I.72, A:W.68, A:W.68 LSM.4: 5 residues within 4Å: Chain A: L.7, G.77, L.81, L.84 Ligands: LSM.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.81, A:L.84 LSM.5: 3 residues within 4Å: Chain A: L.7 Chain C: F.130 Ligands: LSM.4 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:L.7, C:F.130, C:F.130 LSM.6: 4 residues within 4Å: Chain A: F.73, F.74, L.124, A.128 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.74, A:L.124 LSM.7: 11 residues within 4Å: Chain A: Y.59, R.104, L.105, Y.109, A.112, L.115, W.116 Chain B: A.20, L.24, I.27 Ligands: GSH.1 9 PLIP interactions: 1 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:I.27, A:Y.59, A:Y.109, A:A.112, A:L.115, A:W.116, A:W.116 Hydrogen bonds: A:R.104, A:Y.109 LSM.10: 4 residues within 4Å: Chain A: I.72 Chain B: W.68 Ligands: LSM.3, LSM.17 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.72, B:W.68, B:W.68 LSM.11: 5 residues within 4Å: Chain B: L.7, G.77, L.81, L.84 Ligands: LSM.12 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.81, B:L.84 LSM.12: 3 residues within 4Å: Chain A: F.130 Chain B: L.7 Ligands: LSM.11 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.7, A:F.130, A:F.130 LSM.13: 4 residues within 4Å: Chain B: F.73, F.74, L.124, A.128 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.74, B:L.124 LSM.14: 11 residues within 4Å: Chain B: Y.59, R.104, L.105, Y.109, A.112, L.115, W.116 Chain C: A.20, L.24, I.27 Ligands: GSH.8 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:Y.59, B:Y.109, B:A.112, B:L.115, B:W.116, B:W.116, C:I.27 Hydrogen bonds: B:R.104, B:Y.109 LSM.17: 4 residues within 4Å: Chain B: I.72 Chain C: W.68 Ligands: LSM.3, LSM.10 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:I.72, C:W.68, C:W.68 LSM.18: 5 residues within 4Å: Chain C: L.7, G.77, L.81, L.84 Ligands: LSM.19 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.81, C:L.84 LSM.19: 3 residues within 4Å: Chain B: F.130 Chain C: L.7 Ligands: LSM.18 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:L.7, B:F.130, B:F.130 LSM.20: 4 residues within 4Å: Chain C: F.73, F.74, L.124, A.128 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.74, C:L.124 LSM.21: 11 residues within 4Å: Chain A: A.20, L.24, I.27 Chain C: Y.59, R.104, L.105, Y.109, A.112, L.115, W.116 Ligands: GSH.15 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:Y.59, C:Y.109, C:A.112, C:L.115, C:W.116, C:W.116, A:I.27 Hydrogen bonds: C:R.104, C:Y.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saino, H. et al., Seleno-detergent MAD phasing of leukotriene C4 synthase in complex with dodecyl-beta-D-selenomaltoside. Acta Crystallogr.,Sect.F (2011)

Release Date

2011-12-14

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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