SMTL ID : 8s1j.1

Crystal structure of t-anethole oxygenase from Stenotrophomonas maltophilia

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

homo-dimer

Ligands

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 19 residues within 4Å: Chain A: G.57, M.60, M.61, T.65, K.67, R.75, D.78, T.79, H.82, W.86, V.103, I.106, H.107, L.110, T.117, F.118, D.122, T.126, F.165 20 PLIP interactions: 19 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:K.67, A:H.82, A:W.86, A:V.103, A:I.106, A:L.110, A:T.117, A:F.118, A:F.118, A:D.122, A:T.126, A:F.165, A:F.165 Water bridges: A:K.67, A:K.67 Salt bridges: A:K.67, A:R.75 pi-Cation interactions: A:R.75 Metal complexes: A:H.107, H2O.6 HEM.7: 18 residues within 4Å: Chain B: G.57, T.65, K.67, R.75, D.78, T.79, H.82, W.86, V.103, I.106, H.107, L.110, T.117, F.118, D.122, T.126, I.130, F.165 24 PLIP interactions: 23 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:K.67, B:T.79, B:H.82, B:W.86, B:V.103, B:V.103, B:I.106, B:L.110, B:T.117, B:F.118, B:F.118, B:F.118, B:D.122, B:T.126, B:I.130, B:F.165, B:F.165 Water bridges: B:K.67, B:K.67 Salt bridges: B:K.67, B:R.75 pi-Cation interactions: B:R.75 Metal complexes: B:H.107, H2O.12

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: T.30, Y.34, F.134, R.138, G.145, L.146, Q.150, E.265 Ligands: GOL.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.145, A:Q.150, A:Q.150 Water bridges: A:R.138 GOL.3: 7 residues within 4Å: Chain A: L.46, W.129, A.133, R.136, A.140, L.231, Q.232 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.133, A:R.136, A:L.231 Water bridges: A:R.136 GOL.4: 5 residues within 4Å: Chain A: K.8, R.11, Y.34, E.265 Ligands: GOL.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.11, A:Y.34, A:E.265 Water bridges: A:Q.150 GOL.8: 8 residues within 4Å: Chain B: T.30, Y.34, F.134, R.138, G.145, L.146, Q.150, E.265 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.145, B:S.147, B:Q.150, B:Q.150 Water bridges: B:L.29, B:T.30 GOL.9: 6 residues within 4Å: Chain B: L.46, W.129, A.133, R.136, L.231, Q.232 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.133, B:R.136, B:L.137, B:Q.232 Water bridges: B:R.136, B:Q.232

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

CL.5: 4 residues within 4Å: Chain A: R.275, R.278 Chain B: G.218, Q.219 Ligand excluded by PLIP CL.6: 6 residues within 4Å: Chain A: I.26, W.27, T.30, Q.150, A.153, A.154 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: G.218, Q.219 Chain B: R.275, R.278 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Purwani, N.N. et al., Discovery of a new class of bacterial heme-containing CC cleaving oxygenases. N Biotechnol (2024)

Release Date

2024-08-14

Peptides

Trans-anethole oxygenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Trans-anethole oxygenase