SMTL ID : 6y0q.1

Alpha-ketoglutarate-dependent dioxygenase AlkB in complex with Fe, AKG and methylated DNA under anaerobic environment using FT-SSX methods

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

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

AKG.1: 18 residues within 4Å: Chain A: M.61, L.118, N.120, Y.122, L.128, H.131, D.133, S.145, F.154, L.170, H.187, I.189, R.204, N.206, T.208, R.210 Ligands: FE.2, O5W.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.128 Hydrogen bonds: A:N.120, A:Y.122 Water bridges: A:S.145, A:S.145, A:T.208, A:R.210, A:R.210 Salt bridges: A:H.131, A:R.204, A:R.210

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

FE.2: 6 residues within 4Å: Chain A: H.131, D.133, H.187, R.210 Ligands: AKG.1, O5W.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.131, A:D.133, A:H.187, H2O.4

1 x O5W: [(3~{S},5~{R})-5-(6-azanyl-1-methyl-purin-9-yl)-2-(phosphonooxymethyl)oxolan-3-yl] [(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl hydrogen phosphate(Non-covalent)

O5W.3: 22 residues within 4Å: Chain A: T.51, P.52, Y.55, T.56, M.57, S.58, M.61, W.69, Y.76, L.118, K.127, L.128, S.129, L.130, H.131, Q.132, D.133, K.134, D.135, R.210 Ligands: AKG.1, FE.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:T.51 Hydrogen bonds: A:W.69, A:Y.76, A:S.129, A:S.129, A:D.135 Water bridges: A:S.58, A:S.58, A:K.134, A:R.210 pi-Stacking: A:Y.55, A:W.69, A:H.131, A:H.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rabe, P. et al., Anaerobic fixed-target serial crystallography. Iucrj (2020)

Release Date

2020-09-09

Peptides

Alpha-ketoglutarate-dependent dioxygenase AlkB: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Alpha-ketoglutarate-dependent dioxygenase AlkB

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