SMTL ID : 5zmd.2 (1 other biounit)

Crystal structure of FTO in complex with m6dA modified ssDNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

homo-dimer

Ligands

2 x DT- DC- DT- 6MA- DT- DA- DT- DC- DG: DNA (5'-D(P*TP*CP*TP*(6MA)P*TP*AP*TP*CP*G)-3')(Non-covalent)

DT-DC-DT-6MA-DT-DA-DT-DC-DG.1: 38 residues within 4Å: Chain A: R.44, I.49, K.50, K.52, L.54, L.55, P.57, R.60, Y.70, Y.72, L.73, N.74, L.179, K.180, M.190, V.192, S.193, W.194, H.195, H.196, E.198, R.286, R.423, I.424, T.427 Chain B: K.52, Y.178, H.196, S.241, W.242, K.270 Ligands: DT-DC-DT-6MA-DT-DA-DT-DC-DG.2, DT-DC-DT-6MA-DT-DA-DT-DC-DG.2, DT-DC-DT-6MA-DT-DA-DT-DC-DG.2, DT-DC-DT-6MA-DT-DA-DT-DC-DG.2, DT-DC-DT-6MA-DT-DA-DT-DC-DG.2, DT-DC-DT-6MA-DT-DA-DT-DC-DG.2, OGA.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.60, A:R.60, A:S.193, A:E.198 Salt bridges: A:K.270 pi-Cation interactions: A:H.195, A:H.195 DT-DC-DT-6MA-DT-DA-DT-DC-DG.2: 34 residues within 4Å: Chain A: K.52, S.241, W.242, K.270 Chain B: I.49, K.50, K.52, L.54, P.57, R.60, Y.70, Y.72, L.73, N.74, P.177, Y.178, L.179, K.180, M.190, V.192, S.193, W.194, H.195, E.198, K.270, R.286, R.423, I.424, T.427 Ligands: DT-DC-DT-6MA-DT-DA-DT-DC-DG.1, DT-DC-DT-6MA-DT-DA-DT-DC-DG.1, DT-DC-DT-6MA-DT-DA-DT-DC-DG.1, DT-DC-DT-6MA-DT-DA-DT-DC-DG.1, DT-DC-DT-6MA-DT-DA-DT-DC-DG.1 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.60, B:R.60, B:S.193, B:W.194, B:E.198 Salt bridges: B:K.270 pi-Stacking: B:H.195, B:H.195

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 4 residues within 4Å: Chain A: H.195, D.197, H.271 Ligands: OGA.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.195, A:D.197, A:H.271 MN.5: 4 residues within 4Å: Chain B: H.195, D.197, H.271 Ligands: OGA.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.195, B:D.197, B:H.271

2 x OGA: N-OXALYLGLYCINE(Non-covalent)

OGA.4: 14 residues within 4Å: Chain A: R.60, N.169, H.195, D.197, V.208, Y.259, H.271, V.273, R.280, S.282, T.284, R.286 Ligands: DT-DC-DT-6MA-DT-DA-DT-DC-DG.1, MN.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.169, A:Y.259, A:Y.259, A:S.282 Salt bridges: A:R.60, A:H.195, A:R.280, A:R.286 OGA.6: 14 residues within 4Å: Chain B: R.60, N.169, H.195, D.197, V.236, L.253, Y.259, H.271, V.273, R.280, S.282, T.284, R.286 Ligands: MN.5 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.169, B:N.169, B:S.282, B:S.282, B:T.284 Salt bridges: B:R.60, B:H.195, B:R.280, B:R.286

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, X. et al., Structural insights into FTO's catalytic mechanism for the demethylation of multiple RNA substrates. Proc. Natl. Acad. Sci. U.S.A. (2019)

Release Date

2019-04-10

Peptides

Alpha-ketoglutarate-dependent dioxygenase FTO: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
G

Alpha-ketoglutarate-dependent dioxygenase FTO

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