SMTL ID : 6ix5.1

The structure of LepI complex with SAM and its substrate analogue

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

4 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.1: 14 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, L.310, I.311 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.245, A:N.293, A:F.294, A:R.309 Water bridges: A:A.251, A:N.293, A:R.309, A:R.309, A:R.309, A:R.309, A:R.309 Salt bridges: A:R.309 pi-Stacking: A:F.294 SAM.20: 14 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, L.310, I.311 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:G.245, B:G.246, B:N.293, B:F.294 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 SAM.33: 14 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, L.310, I.311 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:G.245, C:N.293, C:F.294, C:R.309 Water bridges: C:A.251, C:N.293, C:R.309, C:R.309, C:R.309, C:R.309, C:R.309 Salt bridges: C:R.309 pi-Stacking: C:F.294 SAM.52: 14 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, L.310, I.311 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:G.245, D:G.246, D:N.293, D:F.294 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: 17 residues within 4Å: Chain A: G.148, H.151, L.156, C.193, F.207, L.210, D.213, R.313, D.314, T.356, C.359, I.360, A.363, L.364 Chain B: F.59, S.66 Ligands: EDO.11 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.156, A:L.156, A:F.207, A:L.210, A:I.360, A:A.363, B:F.59 Hydrogen bonds: A:H.151, A:R.313, A:D.314 Water bridges: A:T.356 pi-Stacking: A:H.151 B0L.21: 20 residues within 4Å: Chain A: F.59, V.62, M.63 Chain B: L.145, G.148, H.151, L.156, C.193, L.197, F.207, L.210, D.213, R.313, D.314, T.356, C.359, I.360, A.363, L.364 Ligands: EDO.27 18 PLIP interactions: 15 interactions with chain B, 3 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 Hydrogen bonds: B:H.151, B:D.314 Water bridges: B:R.313, B:R.313, B:R.313, B:R.313 pi-Stacking: B:H.151 B0L.34: 17 residues within 4Å: Chain C: G.148, H.151, L.156, C.193, F.207, L.210, D.213, R.313, D.314, T.356, C.359, I.360, A.363, L.364 Chain D: F.59, S.66 Ligands: EDO.43 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.156, C:L.156, C:F.207, C:L.210, C:I.360, C:A.363, D:F.59 Hydrogen bonds: C:H.151, C:R.313, C:D.314 pi-Stacking: C:H.151 B0L.53: 20 residues within 4Å: Chain C: F.59, V.62, M.63 Chain D: L.145, G.148, H.151, L.156, C.193, L.197, F.207, L.210, D.213, R.313, D.314, T.356, C.359, I.360, A.363, L.364 Ligands: EDO.59 18 PLIP interactions: 15 interactions with chain D, 3 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 Hydrogen bonds: D:H.151, D:D.314 Water bridges: D:R.313, D:R.313, D:R.313, D:T.356 pi-Stacking: D:H.151

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

EDO.3: 8 residues within 4Å: Chain A: E.108, L.109, R.112 Chain B: P.173, D.174, I.175, V.176, M.361 Ligand excluded by PLIP EDO.4: 3 residues within 4Å: Chain A: K.227, E.228, R.336 Ligand excluded by PLIP EDO.5: 7 residues within 4Å: Chain A: P.173, D.174, I.175, M.361 Chain B: E.108, L.109, R.112 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: S.133, S.134, N.135, Q.138 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: T.212, D.213, E.214 Ligand excluded by PLIP EDO.8: 2 residues within 4Å: Chain A: P.201, T.202 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: Q.301, G.302, P.329, A.330, M.331, D.332 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: L.275, Q.276, Q.279, S.289 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: H.151, L.210 Ligands: B0L.2 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain B: K.85, A.141, P.143 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain B: S.133, S.134, N.135, Q.138 Ligand excluded by PLIP EDO.24: 2 residues within 4Å: Chain B: I.204, K.208 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain B: T.392, W.393, P.394, V.395, N.397 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain B: I.175, V.176, P.316, D.317, G.365, K.367 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain B: H.151, L.210 Ligands: B0L.21 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain A: P.58 Chain B: N.135, Q.138, T.139 Ligand excluded by PLIP EDO.35: 8 residues within 4Å: Chain C: E.108, L.109, R.112 Chain D: P.173, D.174, I.175, V.176, M.361 Ligand excluded by PLIP EDO.36: 3 residues within 4Å: Chain C: K.227, E.228, R.336 Ligand excluded by PLIP EDO.37: 7 residues within 4Å: Chain C: P.173, D.174, I.175, M.361 Chain D: E.108, L.109, R.112 Ligand excluded by PLIP EDO.38: 4 residues within 4Å: Chain C: S.133, S.134, N.135, Q.138 Ligand excluded by PLIP EDO.39: 3 residues within 4Å: Chain C: T.212, D.213, E.214 Ligand excluded by PLIP EDO.40: 2 residues within 4Å: Chain C: P.201, T.202 Ligand excluded by PLIP EDO.41: 6 residues within 4Å: Chain C: Q.301, G.302, P.329, A.330, M.331, D.332 Ligand excluded by PLIP EDO.42: 4 residues within 4Å: Chain C: L.275, Q.276, Q.279, S.289 Ligand excluded by PLIP EDO.43: 3 residues within 4Å: Chain C: H.151, L.210 Ligands: B0L.34 Ligand excluded by PLIP EDO.54: 3 residues within 4Å: Chain D: K.85, A.141, P.143 Ligand excluded by PLIP EDO.55: 4 residues within 4Å: Chain D: S.133, S.134, N.135, Q.138 Ligand excluded by PLIP EDO.56: 2 residues within 4Å: Chain D: I.204, K.208 Ligand excluded by PLIP EDO.57: 5 residues within 4Å: Chain D: T.392, W.393, P.394, V.395, N.397 Ligand excluded by PLIP EDO.58: 6 residues within 4Å: Chain D: I.175, V.176, P.316, D.317, G.365, K.367 Ligand excluded by PLIP EDO.59: 3 residues within 4Å: Chain D: H.151, L.210 Ligands: B0L.53 Ligand excluded by PLIP EDO.60: 4 residues within 4Å: Chain C: P.58 Chain D: N.135, Q.138, T.139 Ligand excluded by PLIP

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

CL.12: 5 residues within 4Å: Chain A: K.347, G.348, A.349 Chain B: R.115, Q.125 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain A: Y.259, P.260, N.261, Q.262 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain A: R.150 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain A: R.215, T.216 Chain B: F.59 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain A: M.161, A.162, K.185 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain B: S.221, T.222, F.223 Ligand excluded by PLIP CL.30: 2 residues within 4Å: Chain B: S.79, R.150 Ligand excluded by PLIP CL.31: 3 residues within 4Å: Chain B: D.80, L.81, G.82 Ligand excluded by PLIP CL.44: 5 residues within 4Å: Chain C: K.347, G.348, A.349 Chain D: R.115, Q.125 Ligand excluded by PLIP CL.45: 4 residues within 4Å: Chain C: Y.259, P.260, N.261, Q.262 Ligand excluded by PLIP CL.46: 1 residues within 4Å: Chain C: R.150 Ligand excluded by PLIP CL.47: 3 residues within 4Å: Chain C: R.215, T.216 Chain D: F.59 Ligand excluded by PLIP CL.48: 3 residues within 4Å: Chain C: M.161, A.162, K.185 Ligand excluded by PLIP CL.61: 3 residues within 4Å: Chain D: S.221, T.222, F.223 Ligand excluded by PLIP CL.62: 2 residues within 4Å: Chain D: S.79, R.150 Ligand excluded by PLIP CL.63: 3 residues within 4Å: Chain D: D.80, L.81, G.82 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.17: 6 residues within 4Å: Chain A: S.54, L.55, E.56, T.57, P.58 Chain B: R.41 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.41 Water bridges: B:R.41, B:R.41, B:N.135, A:E.56 GOL.49: 6 residues within 4Å: Chain C: S.54, L.55, E.56, T.57, P.58 Chain D: R.41 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain D Water bridges: C:E.56, D:R.41, D:R.41, D:N.135 Hydrogen bonds: D:R.41

4 x NA: SODIUM ION(Non-functional Binders)

NA.18: 2 residues within 4Å: Chain A: P.316, D.317 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.317, A:D.317 NA.32: 3 residues within 4Å: Chain B: S.95, A.96, E.97 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.95, B:A.96, B:E.97 NA.50: 2 residues within 4Å: Chain C: P.316, D.317 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.317, C:D.317 NA.64: 3 residues within 4Å: Chain D: S.95, A.96, E.97 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.95, D:A.96, D:E.97

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.19: 7 residues within 4Å: Chain A: L.220, S.221, T.222, F.223, P.224, K.258, Y.259 2 PLIP interactions: 2 interactions with chain A Water bridges: A:L.225, A:Y.259 IMD.51: 7 residues within 4Å: Chain C: L.220, S.221, T.222, F.223, P.224, K.258, Y.259 1 PLIP interactions: 1 interactions with chain C Water bridges: C:L.225

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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