SMTL ID : 8jnr.1

Crystal structure of human ALKBH3 bound to 3mC containing ssDNA through distal crosslink

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.66 Å

Oligo State

hetero-4-4-4-mer

Ligands

2 x DT- ME6- DT: DNA(Non-covalent)

DT-ME6-DT.1: 12 residues within 4Å: Chain A: R.74, Y.79, R.83, Y.93, Y.95, S.96, V.140, C.141, H.143, D.145, E.147 Ligands: OGA.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.95 Hydrogen bonds: A:R.83, A:C.141, A:D.145, A:E.147 Salt bridges: A:R.74 pi-Stacking: A:Y.95, A:H.143 DT-ME6-DT.2: 11 residues within 4Å: Chain D: Y.79, P.82, R.83, Y.93, Y.95, S.96, L.129, V.140, C.141, W.142, H.143 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:Y.95 Hydrogen bonds: D:Y.79, D:Y.93 pi-Stacking: D:Y.95, D:H.143

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

OGA.3: 16 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, T.225, R.227 Ligands: DT-ME6-DT.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:N.223 Salt bridges: A:H.143, A:R.221, A:R.227 OGA.6: 14 residues within 4Å: Chain C: N.131, Y.133, H.143, D.145, F.167, L.191, H.209, V.211, R.221, N.223, T.225, R.227 Ligands: MN.7, ME6.8 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:N.131, C:Y.133, C:Y.133, C:S.158, C:S.158 Salt bridges: C:H.143, C:R.221, C:R.227

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

MN.4: 4 residues within 4Å: Chain A: H.143, D.145, H.209 Ligands: OGA.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.143, A:D.145, A:H.209 MN.5: 3 residues within 4Å: Chain B: H.143, D.145, H.209 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.143, B:D.145, B:H.209 MN.7: 4 residues within 4Å: Chain C: H.143, D.145, H.209 Ligands: OGA.6 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.143, C:D.145, C:H.209 MN.9: 3 residues within 4Å: Chain D: H.143, D.145, H.209 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.143, D:D.145, D:H.209

1 x ME6: [(2R,3S,5R)-5-(4-azanyl-3-methyl-2-oxo-pyrimidin-3-ium-1-yl)-3-hydroxy-oxolan-2-yl]methyl dihydrogen phosphate(Non-covalent)

ME6.8: 12 residues within 4Å: Chain C: R.74, Y.79, R.83, Y.93, Y.95, S.96, L.129, V.140, C.141, H.143, D.145 Ligands: OGA.6 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:R.74, C:Y.79, C:Y.79, C:R.83, C:R.83, C:Y.93, C:S.96, C:D.145 pi-Stacking: C:Y.95, C:H.143

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: ABCD
Synthetic antibody heavy chain: EFGH
Synthetic antibody light chain: IJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

D
E

E
G

F
H

G
I

H
J

I
K

J
L

K
M

L
N

Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3

Synthetic antibody heavy chain

Synthetic antibody light chain

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