SMTL ID : 5ybt.1

Fe(II)/(alpha)ketoglutarate-dependent dioxygenase PrhA-V150L/A232S/M241V in complex with berkeleyone A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

2 x FE: FE (III) ION(Non-covalent)

FE.1: 4 residues within 4Å: Chain A: H.146, D.148, H.230 Ligands: AKG.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.146, A:D.148, A:H.230, H2O.1 FE.4: 4 residues within 4Å: Chain B: H.146, D.148, H.230 Ligands: AKG.5 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.146, B:D.148, B:H.230, H2O.4

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

AKG.2: 12 residues within 4Å: Chain A: R.88, I.134, Q.143, H.146, D.148, F.170, T.183, H.230, A.232, R.242 Ligands: FE.1, 8TC.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.170, A:T.183, A:A.232 Hydrogen bonds: A:Q.143, A:T.183 Water bridges: A:R.88 Salt bridges: A:R.88, A:H.146, A:R.242 AKG.5: 12 residues within 4Å: Chain B: R.88, I.134, Q.143, H.146, D.148, F.170, T.183, H.230, A.232, R.242 Ligands: FE.4, 8TC.6 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.134, B:F.170, B:F.170 Hydrogen bonds: B:Q.143 Water bridges: B:Q.143 Salt bridges: B:R.88, B:H.146, B:R.242

2 x 8TC: berkeleyone A(Non-covalent)

8TC.3: 18 residues within 4Å: Chain A: S.82, N.83, R.88, D.130, M.132, Q.143, R.144, H.146, D.148, L.151, N.168, A.246, S.248 Chain B: C.289, D.292, M.293, V.294 Ligands: AKG.2 13 PLIP interactions: 9 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:D.130, A:D.148, A:L.151, A:A.246, B:D.292, B:V.294, B:V.294 Hydrogen bonds: A:S.82, A:Q.143, A:R.144, A:D.148, B:D.292 Salt bridges: A:R.88 8TC.6: 17 residues within 4Å: Chain A: C.289, D.292, M.293, V.294 Chain B: S.82, N.83, R.88, D.130, M.132, Q.143, H.146, D.148, L.151, N.168, A.246, S.248 Ligands: AKG.5 11 PLIP interactions: 3 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:D.292, A:V.294, B:D.130, B:D.148, B:L.151, B:A.246 Hydrogen bonds: A:D.292, B:Q.143, B:D.148, B:N.168 Salt bridges: B:R.88

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakashima, Y. et al., Structure function and engineering of multifunctional non-heme iron dependent oxygenases in fungal meroterpenoid biosynthesis. Nat Commun (2018)

Release Date

2018-01-24

Peptides

PrhA: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PrhA