SMTL ID : 7cy7.1

Crystal Structure of CMD1 in complex with DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 3 residues within 4Å: Chain A: N.219, T.238, S.239 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.219, A:T.238, A:T.238 EDO.2: 5 residues within 4Å: Chain A: A.470, I.471, Q.472, S.473, W.574 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.470, A:Q.472, A:S.473 Water bridges: A:A.470 EDO.3: 4 residues within 4Å: Chain A: T.489, E.539, Q.590, R.679 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.489, A:E.539, A:R.679 EDO.4: 5 residues within 4Å: Chain A: K.642, R.651, K.659, D.662, D.812 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.642, A:K.642 EDO.5: 6 residues within 4Å: Chain A: E.670, W.673, S.674, E.677, R.687, A.702 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.670, A:R.687, A:A.702 Water bridges: A:E.677 EDO.6: 5 residues within 4Å: Chain A: K.520, W.521, D.622, G.715, M.717 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.521, A:G.715 EDO.7: 5 residues within 4Å: Chain A: D.688, L.689, I.691, T.692, V.861 No protein-ligand interaction detected (PLIP) EDO.8: 5 residues within 4Å: Chain A: L.632, I.633, Q.634, N.635, K.794 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.632, A:Q.634, A:Q.634, A:N.635

1 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.9: 4 residues within 4Å: Chain A: R.514, F.619, H.719, L.720 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.619 Hydrogen bonds: A:L.720

1 x FE2: FE (II) ION(Non-covalent)

FE2.10: 4 residues within 4Å: Chain A: R.618, H.719, D.721, H.771 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.719, A:D.721, A:H.771, H2O.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, W. et al., Molecular mechanism for vitamin C-derived C 5 -glyceryl-methylcytosine DNA modification catalyzed by algal TET homologue CMD1. Nat Commun (2021)

Release Date

2020-12-30

Peptides

Maltodextrin-binding protein,5-methylcytosine-modifying enzyme 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Maltodextrin-binding protein,5-methylcytosine-modifying enzyme 1

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