SMTL ID : 7cy5.1

Crystal Structure of CMD1 in complex with vitamin C

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x FE: FE (III) ION(Non-covalent)

FE.1: 4 residues within 4Å: Chain A: H.719, D.721, H.771 Ligands: ASC.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.719, A:D.721, A:H.771, H2O.5

1 x ASC: ASCORBIC ACID(Non-covalent)

ASC.2: 13 residues within 4Å: Chain A: S.709, T.711, V.716, H.719, I.730, F.745, H.771, G.772, T.773, G.786, S.787, S.788 Ligands: FE.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.709, A:S.709, A:T.711, A:H.719, A:T.773, A:S.788 Water bridges: A:W.732, A:S.788

2 x CIT: CITRIC ACID(Non-functional Binders)

CIT.3: 5 residues within 4Å: Chain A: E.112, Y.156, F.157, W.231 Ligands: CIT.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.156 CIT.4: 7 residues within 4Å: Chain A: E.154, P.155, Y.156, M.331, W.341, R.345 Ligands: CIT.3 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.156, A:W.341 Hydrogen bonds: A:Y.156 Salt bridges: A:R.345

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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