SMTL ID : 7etk.1

The complex structure of FtmOx1 bond with fumitremorgen B at 1.22 angstrom

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.22 Å

Oligo State

homo-dimer

Ligands

2 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.1: 12 residues within 4Å: Chain A: F.115, R.117, Q.126, H.129, D.131, T.166, H.205, G.207, R.218, V.220 Ligands: FE2.2, 4Q1.7 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.126 Water bridges: A:R.218 Salt bridges: A:R.117, A:R.117, A:H.129, A:R.218 AKG.9: 13 residues within 4Å: Chain B: F.115, R.117, Q.126, H.129, D.131, T.166, H.205, G.207, R.218, V.220, L.222 Ligands: FE2.10, 4Q1.12 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Q.126, B:Q.126, B:T.166 Water bridges: B:R.218 Salt bridges: B:R.117, B:R.117, B:H.129, B:R.218

4 x FE2: FE (II) ION(Non-covalent)

FE2.2: 4 residues within 4Å: Chain A: H.129, D.131, H.205 Ligands: AKG.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.129, A:D.131, A:H.205, H2O.1 FE2.3: 1 residues within 4Å: Chain A: E.162 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.162, H2O.10, H2O.10 FE2.10: 4 residues within 4Å: Chain B: H.129, D.131, H.205 Ligands: AKG.9 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.129, B:D.131, B:H.205, H2O.11 FE2.11: 1 residues within 4Å: Chain B: E.161 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.161, H2O.19, H2O.20

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

EDO.4: 3 residues within 4Å: Chain A: W.175, T.176, E.177 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.176, A:T.176, A:E.177 EDO.5: 2 residues within 4Å: Chain A: R.105 Chain B: Y.140 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.105, B:Y.140 EDO.6: 5 residues within 4Å: Chain A: C.22, L.25, E.26, A.101, Y.102 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.101

2 x 4Q1: fumitremorgen B(Non-covalent)

4Q1.7: 16 residues within 4Å: Chain A: Y.68, F.72, Y.74, F.115, R.117, Q.126, P.127, F.128, H.129, R.130, D.131, A.133, T.134, L.222, F.233 Ligands: AKG.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.72, A:A.133, A:T.134, A:L.222, A:F.233 Hydrogen bonds: A:R.117, A:H.129 pi-Stacking: A:Y.68 4Q1.12: 17 residues within 4Å: Chain B: L.64, Y.68, F.72, Y.74, F.115, R.117, Q.126, P.127, F.128, H.129, R.130, D.131, A.133, T.134, L.222, F.233 Ligands: AKG.9 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:A.133, B:T.134, B:L.222, B:F.233 Hydrogen bonds: B:R.117, B:Q.126, B:H.129 Water bridges: B:Y.68 pi-Stacking: B:F.72, B:H.129

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 5 residues within 4Å: Chain A: P.232, T.235, R.237 Chain B: P.232, N.271 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.237, B:N.271, B:N.271 Water bridges: A:T.235, A:T.235 GOL.13: 3 residues within 4Å: Chain B: W.175, T.176, E.177 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.176, B:E.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, L. et al., Structural Insight into the Catalytic Mechanism of the Endoperoxide Synthase FtmOx1. Angew.Chem.Int.Ed.Engl. (2022)

Release Date

2021-12-01

Peptides

Verruculogen synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Verruculogen synthase