SMTL ID : 8jnk.1 (1 other biounit)

Crystal structure of human ALKBH3 bound to ssDNA through active site crosslink

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.69 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x DT- 2YR- DT- DA- DC- DG: DNA(Non-covalent)

DT-2YR-DT-DA-DC-DG.1: 23 residues within 4Å: Chain A: R.74, E.75, I.77, Y.79, P.82, R.83, Y.93, T.94, Y.95, S.96, R.97, S.139, V.140, D.141, W.142, H.143, D.145, C.147, L.150, K.213, E.214, Y.215 Ligands: OGA.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:H.143 Hydrogen bonds: A:R.83, A:D.141, A:S.144 Salt bridges: A:R.74 pi-Stacking: A:H.143 DT-2YR-DT-DA-DC-DG.2: 19 residues within 4Å: Chain B: R.74, E.75, Y.79, P.82, R.83, Y.93, Y.95, S.96, K.137, S.139, V.140, D.141, W.142, H.143, D.145, C.147, K.213, Y.215 Ligands: OGA.5 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:H.143 Hydrogen bonds: B:R.83, B:D.141, B:D.145 pi-Stacking: B:H.143

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

OGA.3: 14 residues within 4Å: Chain A: L.129, N.131, Y.133, H.143, D.145, F.167, L.191, H.209, V.211, R.221, N.223, R.227 Ligands: DT-2YR-DT-DA-DC-DG.1, MN.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.131, A:N.131, A:Y.133 Salt bridges: A:H.143, A:R.221, A:R.227 OGA.5: 14 residues within 4Å: Chain B: L.129, N.131, Y.133, H.143, D.145, S.158, F.167, H.209, V.211, R.221, N.223, R.227 Ligands: 2YR-DT-DA-DC-DG.2, MN.6 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.131, B:Y.133, B:Y.133, B:Y.133, B:D.145, B:S.158 Salt bridges: B:H.143, B:R.221, B:R.227

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

MN.4: 4 residues within 4Å: Chain A: H.143, D.145, H.209 Ligands: OGA.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.143, A:D.145, A:D.145, A:H.209 MN.6: 4 residues within 4Å: Chain B: H.143, D.145, H.209 Ligands: OGA.5 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.143, B:D.145, B:D.145, B:H.209

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, L. et al., The Molecular Basis of Human ALKBH3 Mediated RNA N 1 -methyladenosine (m 1 A) Demethylation. Angew.Chem.Int.Ed.Engl. (2024)

Release Date

2024-01-24

Peptides

Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3: AB
Synthetic antibody heavy chain: CD
Synthetic antibody light chain: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
G

C
I

D
K

E
M

F
O

Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3

Synthetic antibody heavy chain

Synthetic antibody light chain

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