SMTL ID : 6ix8.1

The structure of LepI C52A in complex with SAM and its substrate analogue

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 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:G.246, A:N.293, A:F.294 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.9: 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 12 PLIP interactions: 12 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 Salt bridges: B:R.309 pi-Stacking: B:F.294 SAM.17: 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:G.246, C:N.293, C:F.294 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.25: 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 12 PLIP interactions: 12 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 Salt bridges: D:R.309 pi-Stacking: D:F.294

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

CL.2: 4 residues within 4Å: Chain A: Y.259, P.260, N.261, Q.262 Ligand excluded by PLIP CL.3: 5 residues within 4Å: Chain A: K.347, G.348, A.349 Chain B: R.115, Q.125 Ligand excluded by PLIP CL.4: 5 residues within 4Å: Chain A: R.265, M.290, V.300 Chain C: P.299 Ligands: CL.20 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: S.133, S.134 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.20: 5 residues within 4Å: Chain A: P.299 Chain C: R.265, M.290, V.300 Ligands: CL.4 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain C: S.133, S.134 Ligand excluded by PLIP

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

NA.6: 4 residues within 4Å: Chain A: G.348, A.349 Chain B: A.118, S.119 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.348 Water bridges: A:A.349 NA.7: 2 residues within 4Å: Chain A: E.346, K.347 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.346 NA.14: 3 residues within 4Å: Chain B: P.93, T.126, D.128 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.128 NA.22: 4 residues within 4Å: Chain C: G.348, A.349 Chain D: A.118, S.119 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.349 Water bridges: C:A.349 NA.23: 2 residues within 4Å: Chain C: E.346, K.347 1 PLIP interactions: 1 interactions with chain C Water bridges: C:E.346 NA.30: 3 residues within 4Å: Chain D: P.93, T.126, D.128 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.126, D:T.126

4 x B3O: (1R,2R,4aS,8S,8aR)-2,8-dimethyl-5'-phenyl-4a,5,6,7,8,8a-hexahydro-2H,2'H-spiro[naphthalene-1,3'-pyridine]-2',4'(1'H)-dione(Non-covalent)

B3O.8: 15 residues within 4Å: Chain A: H.151, L.156, C.193, F.207, R.215, R.313, D.314, T.356, C.359, I.360, A.363, L.364 Chain B: M.63, S.66, L.67 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.156, A:F.207, A:I.360, A:A.363, B:L.67 Hydrogen bonds: A:R.313, A:D.314 pi-Stacking: A:H.151 B3O.16: 15 residues within 4Å: Chain A: M.63, S.66, L.67 Chain B: H.151, L.156, C.193, L.197, F.207, R.313, D.314, T.356, C.359, I.360, A.363, L.364 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.156, B:L.197, B:F.207, B:T.356, B:I.360, B:A.363, A:L.67 Hydrogen bonds: B:R.313, B:D.314 pi-Stacking: B:H.151 B3O.24: 15 residues within 4Å: Chain C: H.151, L.156, C.193, F.207, R.215, R.313, D.314, T.356, C.359, I.360, A.363, L.364 Chain D: M.63, S.66, L.67 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.156, C:F.207, C:I.360, C:A.363, D:L.67 Hydrogen bonds: C:R.313, C:D.314 pi-Stacking: C:H.151 B3O.32: 15 residues within 4Å: Chain C: M.63, S.66, L.67 Chain D: H.151, L.156, C.193, L.197, F.207, R.313, D.314, T.356, C.359, I.360, A.363, L.364 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.156, D:L.197, D:F.207, D:T.356, D:I.360, D:A.363, C:L.67 Hydrogen bonds: D:R.313, D:D.314 pi-Stacking: D:H.151

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

EDO.10: 8 residues within 4Å: Chain A: E.108, L.109, R.112 Chain B: P.173, D.174, I.175, V.176, M.361 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:P.173, B:I.175, A:R.112 EDO.11: 4 residues within 4Å: Chain A: T.354, D.357 Chain B: R.112, R.115 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.357 Water bridges: A:D.357, A:K.367, A:K.367, A:Q.373, A:Q.373, B:R.115 EDO.12: 1 residues within 4Å: Chain B: W.393 No protein-ligand interaction detected (PLIP) EDO.13: 8 residues within 4Å: Chain A: P.173, D.174, I.175, V.176, M.361 Chain B: E.108, L.109, R.112 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:P.173, A:I.175, B:R.112 EDO.26: 8 residues within 4Å: Chain C: E.108, L.109, R.112 Chain D: P.173, D.174, I.175, V.176, M.361 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:P.173, D:I.175, C:R.112 EDO.27: 4 residues within 4Å: Chain C: T.354, D.357 Chain D: R.112, R.115 7 PLIP interactions: 2 interactions with chain D, 5 interactions with chain C Water bridges: D:R.115, D:Y.116, C:K.367, C:K.367, C:Q.373, C:Q.373 Hydrogen bonds: C:D.357 EDO.28: 1 residues within 4Å: Chain D: W.393 No protein-ligand interaction detected (PLIP) EDO.29: 8 residues within 4Å: Chain C: P.173, D.174, I.175, V.176, M.361 Chain D: E.108, L.109, R.112 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:R.112, C:P.173, C:I.175

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.15: 3 residues within 4Å: Chain B: R.265, M.290, P.299 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.299 Salt bridges: B:R.265 ACT.31: 3 residues within 4Å: Chain D: R.265, M.290, P.299 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:P.299 Salt bridges: D:R.265

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

Related Entries With Identical Sequence