SMTL ID : 6vya.6 (5 other biounits)

Crystal structure of NotF in complex with brevianamide F and DMSPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-tetramer

Ligands

4 x QRP: (3S,8aS)-3-(1H-indol-3-ylmethyl)hexahydropyrrolo[1,2-a]pyrazine-1,4-dione(Non-covalent)

QRP.1: 13 residues within 4Å: Chain A: T.119, I.120, S.121, E.128, G.144, L.213, A.218, Y.234, F.236, Y.286, F.288, W.444 Ligands: DST.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.120, A:L.213, A:Y.234, A:F.236, A:Y.286, A:F.288 QRP.3: 12 residues within 4Å: Chain B: T.119, I.120, S.121, E.128, G.144, L.213, Y.234, F.236, Y.286, F.288, W.444 Ligands: DST.4 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.120, B:L.213, B:F.236, B:Y.286, B:F.288 Hydrogen bonds: B:E.128 pi-Stacking: B:Y.234 QRP.5: 13 residues within 4Å: Chain C: T.119, I.120, S.121, E.128, G.144, L.213, A.218, Y.234, F.236, Y.286, F.288, W.444 Ligands: DST.6 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:I.120, C:L.213, C:Y.234, C:F.236, C:Y.286, C:F.288, C:F.288 QRP.7: 14 residues within 4Å: Chain D: T.119, I.120, S.121, R.122, E.128, G.144, L.213, A.218, Y.234, F.236, Y.286, F.288, W.444 Ligands: DST.8 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:I.120, D:L.213, D:Y.286, D:F.288 pi-Stacking: D:Y.234

4 x DST: DIMETHYLALLYL S-THIOLODIPHOSPHATE(Covalent)

DST.2: 13 residues within 4Å: Chain A: E.128, R.142, K.232, Y.234, F.288, K.302, Y.304, I.374, K.389, Y.391, W.444, Y.460 Ligands: QRP.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.304, A:I.374 Hydrogen bonds: A:Y.234, A:Y.304 Salt bridges: A:R.142, A:K.232, A:K.302, A:K.389 DST.4: 13 residues within 4Å: Chain B: E.128, R.142, K.232, Y.234, F.288, K.302, Y.304, I.374, K.389, Y.391, W.444, Y.460 Ligands: QRP.3 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.304, B:I.374, B:Y.391 Hydrogen bonds: B:Y.304, B:K.389, B:Y.391, B:Y.460 Salt bridges: B:R.142, B:K.232, B:K.302, B:K.389 DST.6: 13 residues within 4Å: Chain C: E.128, R.142, K.232, Y.234, F.288, K.302, Y.304, I.374, K.389, Y.391, W.444, Y.460 Ligands: QRP.5 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:Y.304, C:I.374 Hydrogen bonds: C:Y.234, C:Y.304 Salt bridges: C:R.142, C:K.232, C:K.302, C:K.389 DST.8: 13 residues within 4Å: Chain D: E.128, R.142, K.232, Y.234, F.288, K.302, Y.304, I.374, K.389, Y.391, W.444, Y.460 Ligands: QRP.7 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:Y.304, D:I.374 Hydrogen bonds: D:R.142, D:Y.304, D:Y.391, D:Y.460 Salt bridges: D:R.142, D:K.232, D:K.302, D:K.389

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kelly, S.P. et al., Data Science-Driven Analysis of Substrate-Permissive Diketopiperazine Reverse Prenyltransferase NotF: Applications in Protein Engineering and Cascade Biocatalytic Synthesis of (-)-Eurotiumin A. J.Am.Chem.Soc. (2022)

Release Date

2021-02-03

Peptides

Deoxybrevianamide E synthase notF: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
Q

B
R

C
S

D
T

Deoxybrevianamide E synthase notF

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