SMTL ID : 8jnk.2 (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 2YR- DT- DA- DC- DG: DNA(Non-covalent)

2YR-DT-DA-DC-DG.1: 17 residues within 4Å: Chain A: Y.79, P.82, R.83, Y.93, T.94, Y.95, S.96, S.139, V.140, D.141, W.142, H.143, D.145, C.147, L.150, K.213 Ligands: OGA.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.95, A:Y.95, A:H.143 Hydrogen bonds: A:Y.93, A:S.96, A:D.141 pi-Stacking: A:H.143 2YR-DT-DA-DC-DG.2: 18 residues within 4Å: Chain B: Y.79, P.82, R.83, Y.95, S.96, K.137, S.139, V.140, D.141, W.142, H.143, S.144, D.145, D.146, C.147, P.148, L.150, K.213 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:H.143 Hydrogen bonds: B:R.83, B:S.96, B:S.96, B:D.141 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, S.158, F.167, L.191, H.209, V.211, R.221, N.223 Ligands: 2YR-DT-DA-DC-DG.1, MN.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.131, A:N.131, A:Y.133, A:S.158, A:S.158 Salt bridges: A:H.143, A:R.221, A:R.227 OGA.5: 15 residues within 4Å: Chain B: L.129, N.131, Y.133, H.143, D.145, S.158, F.167, L.191, H.209, V.211, R.221, N.223, T.225, R.227 Ligands: MN.6 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.131, B:Y.133, B:Y.133, B:S.158, B:N.223 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: 5 residues within 4Å: Chain B: H.143, D.145, H.209, R.227 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
C

B
E

C
J

D
L

E
N

F
P

Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3

Synthetic antibody heavy chain

Synthetic antibody light chain

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