SMTL ID : 5zm4.1 (1 other biounit)

Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AndA with preandiloid C

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

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

FE.1: 4 residues within 4Å: Chain A: H.148, D.150, H.226 Ligands: AKG.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.148, A:D.150, A:H.226, H2O.2 FE.4: 4 residues within 4Å: Chain B: H.148, D.150, H.226 Ligands: AKG.5 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.148, B:D.150, B:H.226, H2O.8

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

AKG.2: 13 residues within 4Å: Chain A: I.84, H.92, L.136, Q.145, H.148, D.150, T.186, H.226, G.227, G.228, R.237 Ligands: FE.1, 9FU.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.145, A:T.186, A:G.228 Water bridges: A:T.186 Salt bridges: A:H.92, A:H.148, A:R.237 AKG.5: 13 residues within 4Å: Chain B: I.84, H.92, L.136, M.138, Q.145, H.148, D.150, T.186, H.226, G.228, R.237 Ligands: FE.4, 9FU.6 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.145, B:G.228 Salt bridges: B:H.92, B:H.148, B:R.237

2 x 9FU: (6aS,8aR,12aS,12bR,13aR)-5,6a,9,9,12a,13a-hexamethyl-7,8,8a,9,12a,12b,13,13a-octahydro-3H-benzo[a]furo[3,4-j]xanthene-3,4,10(1H,6aH)-trione(Non-covalent)

9FU.3: 19 residues within 4Å: Chain A: E.79, Q.80, T.81, I.83, I.84, M.86, H.92, N.131, M.132, N.134, L.136, D.150, L.153, N.171, A.241, A.243, R.252 Chain B: Y.285 Ligands: AKG.2 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.84, A:I.84, A:L.136, A:L.153, A:L.153, B:Y.285, B:Y.285 Hydrogen bonds: A:I.84, A:N.134 9FU.6: 19 residues within 4Å: Chain A: Y.285 Chain B: E.79, Q.80, T.81, I.83, I.84, M.86, N.131, M.132, N.134, L.136, D.150, L.153, M.169, N.171, A.241, A.243, R.252 Ligands: AKG.5 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.84, B:L.136, B:L.153, B:L.153, A:Y.285, A:Y.285 Hydrogen bonds: B:I.84, B:N.134 Water bridges: A:Y.285

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakashima, Y. et al., Structural and Computational Bases for Dramatic Skeletal Rearrangement in Anditomin Biosynthesis. J. Am. Chem. Soc. (2018)

Release Date

2018-07-18

Peptides

Dioxygenase andA: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dioxygenase andA

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