SMTL ID : 6ix7.1

The structure of LepI C52A in complex with SAH and substrate analogue

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

homo-tetramer

Ligands

4 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 13 residues within 4Å: Chain A: L.211, G.245, G.246, G.247, D.270, L.271, V.274, H.292, N.293, F.294, H.295, R.309, I.311 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.246, A:G.247, A:N.293, A:F.294, A:R.309 Water bridges: A:M.248, A:A.251, A:R.309, A:R.309, A:R.309 Salt bridges: A:R.309 pi-Stacking: A:F.294 SAH.8: 13 residues within 4Å: Chain B: L.211, G.245, G.246, G.247, D.270, L.271, V.274, H.292, N.293, F.294, H.295, R.309, I.311 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:N.293, B:F.294, B:R.309, B:R.309 Water bridges: B:A.251, B:N.293, B:R.309, B:R.309, B:R.309, B:R.309, B:R.309 Salt bridges: B:R.309 pi-Stacking: B:F.294 SAH.16: 13 residues within 4Å: Chain C: L.211, G.245, G.246, G.247, D.270, L.271, V.274, H.292, N.293, F.294, H.295, R.309, I.311 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:G.246, C:G.247, C:N.293, C:F.294, C:R.309 Water bridges: C:M.248, C:A.251, C:R.309, C:R.309, C:R.309 Salt bridges: C:R.309 pi-Stacking: C:F.294 SAH.23: 13 residues within 4Å: Chain D: L.211, G.245, G.246, G.247, D.270, L.271, V.274, H.292, N.293, F.294, H.295, R.309, I.311 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:N.293, D:F.294, D:R.309, D:R.309 Water bridges: D:A.251, D:N.293, D:R.309, D:R.309, D:R.309, D:R.309, D:R.309 Salt bridges: D:R.309 pi-Stacking: D:F.294

4 x B0L: 4-hydroxy-3-[(2S,6E,8E)-2-methyldeca-6,8-dienoyl]-5-phenylpyridin-2(1H)-one(Non-covalent)

B0L.2: 19 residues within 4Å: Chain A: L.145, H.151, L.156, C.193, L.197, F.207, D.213, R.313, D.314, T.356, C.359, I.360, A.363, L.364 Chain B: F.59, V.62, M.63 Ligands: GOL.6, EDO.7 17 PLIP interactions: 13 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.145, A:L.156, A:L.156, A:L.197, A:F.207, A:I.360, A:A.363, B:F.59, B:F.59, B:V.62, B:M.63 Hydrogen bonds: A:H.151, A:D.314 Water bridges: A:R.313, A:R.313, A:R.313 pi-Stacking: A:H.151 B0L.9: 19 residues within 4Å: Chain A: F.59, V.62, M.63 Chain B: L.145, H.151, L.156, C.193, L.197, F.207, L.210, R.313, D.314, T.356, C.359, I.360, A.363, L.364 Ligands: GOL.12, EDO.15 18 PLIP interactions: 14 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.145, B:L.156, B:L.156, B:L.197, B:F.207, B:L.210, B:I.360, B:A.363, A:F.59, A:F.59, A:V.62, A:M.63 Hydrogen bonds: B:H.151, B:D.314 Water bridges: B:R.313, B:R.313, B:R.313 pi-Stacking: B:H.151 B0L.17: 19 residues within 4Å: Chain C: L.145, H.151, L.156, C.193, L.197, F.207, D.213, R.313, D.314, T.356, C.359, I.360, A.363, L.364 Chain D: F.59, V.62, M.63 Ligands: GOL.21, EDO.22 17 PLIP interactions: 13 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:L.145, C:L.156, C:L.156, C:L.197, C:F.207, C:I.360, C:A.363, D:F.59, D:F.59, D:V.62, D:M.63 Hydrogen bonds: C:H.151, C:D.314 Water bridges: C:R.313, C:R.313, C:R.313 pi-Stacking: C:H.151 B0L.24: 19 residues within 4Å: Chain C: F.59, V.62, M.63 Chain D: L.145, H.151, L.156, C.193, L.197, F.207, L.210, R.313, D.314, T.356, C.359, I.360, A.363, L.364 Ligands: GOL.27, EDO.30 18 PLIP interactions: 14 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:L.145, D:L.156, D:L.156, D:L.197, D:F.207, D:L.210, D:I.360, D:A.363, C:F.59, C:F.59, C:V.62, C:M.63 Hydrogen bonds: D:H.151, D:D.314 Water bridges: D:R.313, D:R.313, D:R.313 pi-Stacking: D:H.151

8 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: Y.259, P.260, N.261, Q.262 Ligand excluded by PLIP CL.4: 5 residues within 4Å: Chain A: K.347, G.348, A.349 Chain B: R.115, Q.125 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain B: R.215, T.216 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain B: S.221, T.222, F.223 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain C: Y.259, P.260, N.261, Q.262 Ligand excluded by PLIP CL.19: 5 residues within 4Å: Chain C: K.347, G.348, A.349 Chain D: R.115, Q.125 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain D: R.215, T.216 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain D: S.221, T.222, F.223 Ligand excluded by PLIP

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: A.42, D.46, P.394, V.395 Chain B: D.60 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.42, A:D.46, A:D.46 Water bridges: A:V.395 GOL.6: 8 residues within 4Å: Chain A: R.215, R.313, A.352, T.356, V.395, N.397 Chain B: M.63 Ligands: B0L.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.215, A:R.215, A:R.313, A:T.356, A:T.356, A:N.397 Water bridges: A:R.313 GOL.12: 9 residues within 4Å: Chain A: M.63 Chain B: R.215, R.313, A.352, T.356, V.395, N.397 Ligands: B0L.9, EDO.13 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.215, B:R.215, B:R.313, B:T.356, B:N.397 Water bridges: B:R.313, B:N.397 GOL.20: 5 residues within 4Å: Chain C: A.42, D.46, P.394, V.395 Chain D: D.60 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:A.42, C:D.46, C:D.46 Water bridges: C:D.46, C:V.395 GOL.21: 8 residues within 4Å: Chain C: R.215, R.313, A.352, T.356, V.395, N.397 Chain D: M.63 Ligands: B0L.17 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.215, C:R.215, C:R.313, C:T.356, C:N.397 Water bridges: C:R.313 GOL.27: 9 residues within 4Å: Chain C: M.63 Chain D: R.215, R.313, A.352, T.356, V.395, N.397 Ligands: B0L.24, EDO.28 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:R.215, D:R.215, D:R.313, D:T.356, D:T.356, D:N.397 Water bridges: D:R.313, D:N.397

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

EDO.7: 4 residues within 4Å: Chain A: H.151, L.210, R.313 Ligands: B0L.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.313 EDO.13: 7 residues within 4Å: Chain B: T.392, W.393, P.394, V.395, N.397 Ligands: GOL.12, EDO.14 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.392, B:W.393, B:V.395, B:N.397 EDO.14: 6 residues within 4Å: Chain A: D.60 Chain B: A.42, D.46, P.394, V.395 Ligands: EDO.13 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.46, B:W.351 EDO.15: 2 residues within 4Å: Chain B: L.210 Ligands: B0L.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.313 EDO.22: 4 residues within 4Å: Chain C: H.151, L.210, R.313 Ligands: B0L.17 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.313 EDO.28: 7 residues within 4Å: Chain D: T.392, W.393, P.394, V.395, N.397 Ligands: GOL.27, EDO.29 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:W.393, D:V.395, D:N.397 EDO.29: 6 residues within 4Å: Chain C: D.60 Chain D: A.42, D.46, P.394, V.395 Ligands: EDO.28 2 PLIP interactions: 2 interactions with chain D Water bridges: D:D.46, D:W.351 EDO.30: 2 residues within 4Å: Chain D: L.210 Ligands: B0L.24 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.313

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cai, Y. et al., Structural basis for stereoselective dehydration and hydrogen-bonding catalysis by the SAM-dependent pericyclase LepI. Nat.Chem. (2019)

Release Date

2019-07-17

Peptides

O-methyltransferase lepI: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

O-methyltransferase lepI

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