SMTL ID : 7v4g.2 (2 other biounits)

Crystal structure of human ALKBH5 in complex with m6A-containing ssRNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

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

G-G-6MZ-C.1: 25 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: GOL.2, GOL.4, SO4.5 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

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 1 residues within 4Å: Ligands: G-G-6MZ-C.1 No protein-ligand interaction detected (PLIP) GOL.4: 6 residues within 4Å: Chain A: Y.69, G.70, A.71, Q.72 Ligands: G-G-6MZ-C.1, G-G-6MZ-C.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.69, A:A.71

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

MN.3: 4 residues within 4Å: Chain A: H.132, D.134, H.194 Ligands: SO4.5 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 SO4: SULFATE ION(Non-functional Binders)

SO4.5: 11 residues within 4Å: Chain A: K.60, Y.67, N.121, I.129, H.132, D.134, H.194, I.209, R.211 Ligands: G-G-6MZ-C.1, MN.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.67, A:N.121 Water bridges: A:R.211, A:R.211 Salt bridges: A:K.60, A:H.132, A:R.211

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
B

RNA demethylase ALKBH5

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