SMTL ID : 4jrz.1

Human LTC4 synthase in complex with product analogs - implications for enzyme catalysis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 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.12, NI.23 6 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, 2 interactions with chain C Metal complexes: A:H.5, A:H.7, B:H.5, B:H.7, C:H.5, C: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.12: 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.23 6 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, 2 interactions with chain C Metal complexes: A:H.5, A:H.7, B:H.5, B:H.7, C:H.5, C:H.7 NI.13: 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.14: 3 residues within 4Å: Chain B: H.3, H.4, H.5 No protein-ligand interaction detected (PLIP) NI.23: 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.12 6 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B, 2 interactions with chain A Metal complexes: C:H.5, C:H.7, B:H.5, B:H.7, A:H.5, A:H.7 NI.24: 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.25: 3 residues within 4Å: Chain C: H.3, H.4, H.5 No protein-ligand interaction detected (PLIP)

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

SO4.4: 4 residues within 4Å: Chain A: R.54, S.106, A.107, Q.108 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.54, A:S.106, A:A.107, A:Q.108 SO4.15: 4 residues within 4Å: Chain B: R.54, S.106, A.107, Q.108 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.54, B:S.106, B:A.107, B:Q.108 SO4.26: 4 residues within 4Å: Chain C: R.54, S.106, A.107, Q.108 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.54, C:S.106, C:A.107, C:Q.108

3 x PAM: PALMITOLEIC ACID(Non-covalent)

PAM.5: 10 residues within 4Å: Chain A: H.7, E.10, V.11, W.74, I.78 Chain C: H.6, K.8, W.74 Ligands: PAM.16, PAM.27 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:H.7, A:V.11, C:W.74, C:W.74 Hydrogen bonds: A:E.10 Water bridges: C:K.8 Salt bridges: C:K.8 PAM.16: 10 residues within 4Å: Chain A: H.6, K.8, W.74 Chain B: H.7, E.10, V.11, W.74, I.78 Ligands: PAM.5, PAM.27 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.74, A:W.74, B:H.7, B:V.11 Water bridges: A:K.8 Salt bridges: A:K.8 PAM.27: 10 residues within 4Å: Chain B: H.6, K.8, W.74 Chain C: H.7, E.10, V.11, W.74, I.78 Ligands: PAM.5, PAM.16 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:W.74, B:W.74, C:H.7, C:V.11 Water bridges: B:K.8 Salt bridges: B:K.8

15 x PLM: PALMITIC ACID(Non-covalent)

PLM.6: 2 residues within 4Å: Chain A: L.141, R.142 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.141 PLM.7: 4 residues within 4Å: Chain A: A.129, L.133, F.136 Ligands: PLM.10 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.133, A:F.136, A:F.136 PLM.8: 4 residues within 4Å: Chain A: L.20, Y.27, L.97, Q.101 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.20, A:Y.27, A:L.97 PLM.9: 4 residues within 4Å: Chain C: L.13, V.17, A.86, L.87 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.13, C:V.17, C:L.87 PLM.10: 2 residues within 4Å: Chain A: L.137 Ligands: PLM.7 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.137 PLM.17: 2 residues within 4Å: Chain B: L.141, R.142 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.141 PLM.18: 4 residues within 4Å: Chain B: A.129, L.133, F.136 Ligands: PLM.21 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.133, B:F.136, B:F.136 PLM.19: 4 residues within 4Å: Chain B: L.20, Y.27, L.97, Q.101 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.20, B:Y.27, B:L.97 PLM.20: 4 residues within 4Å: Chain A: L.13, V.17, A.86, L.87 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.13, A:V.17, A:L.87 PLM.21: 2 residues within 4Å: Chain B: L.137 Ligands: PLM.18 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.137 PLM.28: 2 residues within 4Å: Chain C: L.141, R.142 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.141 PLM.29: 4 residues within 4Å: Chain C: A.129, L.133, F.136 Ligands: PLM.32 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.133, C:F.136, C:F.136 PLM.30: 4 residues within 4Å: Chain C: L.20, Y.27, L.97, Q.101 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.20, C:Y.27, C:L.97 PLM.31: 4 residues within 4Å: Chain B: L.13, V.17, A.86, L.87 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.13, B:V.17, B:L.87 PLM.32: 2 residues within 4Å: Chain C: L.137 Ligands: PLM.29 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.137

3 x GTX: S-HEXYLGLUTATHIONE(Non-covalent)

GTX.11: 17 residues within 4Å: Chain A: R.57, N.61, E.64, Y.65, Y.99, R.110, L.114, A.118, F.122 Chain C: A.26, S.29, L.30, V.32, I.33, R.36, Y.56, Q.59 12 PLIP interactions: 7 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:Y.65, A:F.122, C:A.26, C:V.32, C:V.32 Hydrogen bonds: A:R.57, A:N.61, A:E.64, C:S.29 Water bridges: A:Y.103 Salt bridges: A:R.110, C:R.36 GTX.22: 17 residues within 4Å: Chain A: A.26, S.29, L.30, V.32, I.33, R.36, Y.56, Q.59 Chain B: R.57, N.61, E.64, Y.65, Y.99, R.110, L.114, A.118, F.122 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:Y.65, B:F.122, A:A.26, A:V.32, A:V.32 Hydrogen bonds: B:R.57, B:N.61, B:E.64, B:Y.99, A:S.29 Water bridges: B:Y.103 Salt bridges: B:R.110, A:R.36 GTX.33: 17 residues within 4Å: Chain B: A.26, S.29, L.30, V.32, I.33, R.36, Y.56, Q.59 Chain C: R.57, N.61, E.64, Y.65, Y.99, R.110, L.114, A.118, F.122 13 PLIP interactions: 5 interactions with chain B, 8 interactions with chain C Hydrophobic interactions: B:A.26, B:V.32, B:V.32, C:Y.65, C:F.122 Hydrogen bonds: B:S.29, C:R.57, C:N.61, C:E.64, C:Y.99 Salt bridges: B:R.36, C:R.110 Water bridges: C:Y.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Niegowski, D. et al., Crystal Structures of Leukotriene C4 Synthase in Complex with Product Analogs: IMPLICATIONS FOR THE ENZYME MECHANISM. J.Biol.Chem. (2014)

Release Date

2014-01-01

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