SMTL ID : 7wl0.2 (4 other biounits)

Crystal structure of human ALKBH5 in complex with N-oxalylglycine (NOG) and m6A-containing ssRNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x U- G- G- 6MZ- C: RNA (5'-R(*UP*GP*GP*(6MZ)P*CP*UP*GP*C)-3')(Non-covalent)

U-G-G-6MZ-C.1: 23 residues within 4Å: Chain A: P.56, L.57, R.58, K.60, Y.67, Y.69, G.70, R.76, E.81, I.129, V.130, S.131, H.132, V.133, D.134, P.135, F.162, K.163, P.164, I.165, T.193, R.211 Ligands: OGA.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.60, A:K.60, A:Y.67, A:V.130, A:V.130 Water bridges: A:G.70, A:G.70 Salt bridges: A:R.58 pi-Stacking: A:H.132

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

MN.2: 4 residues within 4Å: Chain A: H.132, D.134, H.194 Ligands: OGA.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.132, A:D.134, A:H.194, H2O.1

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

OGA.3: 16 residues within 4Å: Chain A: K.60, Y.67, N.121, Y.123, I.129, H.132, D.134, L.154, H.194, I.196, R.205, V.207, I.209, R.211 Ligands: U-G-G-6MZ-C.1, MN.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.67, A:N.121, A:Y.123 Water bridges: A:R.211, A:R.211 Salt bridges: A:K.60, A:H.132, A:R.205, A:R.211

1 x FMT: FORMIC ACID(Non-functional Binders)

FMT.4: 3 residues within 4Å: Chain A: G.64, G.87, V.89 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.89 Water bridges: A:D.88

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kaur, S. et al., Mechanisms of substrate recognition and N6-methyladenosine demethylation revealed by crystal structures of ALKBH5-RNA complexes. Nucleic Acids Res. (2022)

Release Date

2022-03-30

Peptides

RNA demethylase ALKBH5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

RNA demethylase ALKBH5

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