SMTL ID : 6ix9.1

The structure of LepI C52A in complex with SAM and leporin C

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 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 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.311 Hydrogen bonds: A:G.245, A:N.293, A:F.294, A:R.309 Water bridges: A:G.246, A:M.248, A:H.250, A:N.293, A:R.309, A:R.309, A:R.309, A:R.309 Salt bridges: A:R.309 pi-Stacking: A:F.294 SAM.4: 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:N.293, B:F.294, B:R.309 Water bridges: B:M.248, 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.7: 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 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:I.311 Hydrogen bonds: C:G.245, C:N.293, C:F.294, C:R.309 Water bridges: C:G.246, C:M.248, C:H.250, C:N.293, C:R.309, C:R.309, C:R.309, C:R.309 Salt bridges: C:R.309 pi-Stacking: C:F.294 SAM.10: 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 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:G.245, D:N.293, D:F.294, D:R.309 Water bridges: D:M.248, D:H.250, 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

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

NA.2: 4 residues within 4Å: Chain A: T.354, D.357 Chain B: R.112, Y.116 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.116, A:D.357, A:D.357 NA.8: 4 residues within 4Å: Chain C: T.354, D.357 Chain D: R.112, Y.116 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.112, D:Y.116

2 x B0O: (6R,6aS,10S,10aR)-10-methyl-4-phenyl-6-[(1E)-prop-1-en-1-yl]-2,6,6a,7,8,9,10,10a-octahydro-1H-[2]benzopyrano[4,3-c]pyridin-1-one(Non-covalent)

B0O.3: 15 residues within 4Å: Chain A: M.63, S.66, L.67 Chain B: H.151, C.193, F.194, L.197, F.207, L.210, R.313, D.314, T.356, C.359, I.360, L.364 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.194, B:L.197, B:F.207, A:L.67 Hydrogen bonds: B:R.313, B:D.314 pi-Stacking: B:H.151 B0O.9: 15 residues within 4Å: Chain C: M.63, S.66, L.67 Chain D: H.151, C.193, F.194, L.197, F.207, L.210, R.313, D.314, T.356, C.359, I.360, L.364 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.194, D:L.197, D:F.207, C:L.67 Hydrogen bonds: D:R.313, D:D.314 pi-Stacking: D:H.151

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain B: Q.124, S.133, S.134, N.135, Q.138 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.133, B:N.135, B:Q.138 Water bridges: B:S.133, B:N.135 GOL.11: 5 residues within 4Å: Chain D: Q.124, S.133, S.134, N.135, Q.138 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.133, D:N.135, D:Q.138 Water bridges: D:S.133, D:N.135

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

CL.6: 2 residues within 4Å: Chain B: V.395, N.397 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain D: V.395, N.397 Ligand excluded by PLIP

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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