SMTL ID : 7cy6.1

Crystal Structure of CMD1 in complex with 5mC-DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.1: 7 residues within 4Å: Chain A: A.470, I.471, Q.472, S.473, V.476, S.573, W.574 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.472, A:S.473, A:S.473, A:S.573 Water bridges: A:A.470 PG4.2: 6 residues within 4Å: Chain A: A.444, N.446, R.735, H.736, S.737, K.781 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.444 Hydrogen bonds: A:H.736, A:S.737, A:S.737

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

EDO.3: 6 residues within 4Å: Chain A: E.407, D.477, S.481, L.488, P.490, H.493 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.481, A:S.481 EDO.4: 4 residues within 4Å: Chain A: G.491, R.492, H.493, T.494 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.492 Water bridges: A:T.494, A:T.494, A:Q.538 EDO.5: 5 residues within 4Å: Chain A: L.632, I.633, Q.634, N.635 Chain B: G.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.632, A:Q.634, A:Q.634, A:N.635 EDO.6: 3 residues within 4Å: Chain A: S.466, H.467, D.499 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.466 EDO.7: 4 residues within 4Å: Chain A: D.688, L.689, I.691, T.692 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.693 EDO.8: 2 residues within 4Å: Chain A: T.778, G.780 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.778 Water bridges: A:N.713, A:T.778, A:T.778 EDO.9: 3 residues within 4Å: Chain A: V.663, Q.666, R.667 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.663, A:R.667 Water bridges: A:E.670 EDO.10: 7 residues within 4Å: Chain A: Y.686, A.704, T.705, W.727, I.729, H.789, L.791 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.686, A:H.789, A:L.791 EDO.11: 3 residues within 4Å: Chain A: S.654, N.655, V.656 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.655, A:V.656 EDO.12: 9 residues within 4Å: Chain A: A.650, R.651, S.654, Y.657, G.658, K.659, A.660, N.661, D.662 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.654, A:S.654, A:K.659, A:N.661, A:N.661, A:D.662 EDO.13: 3 residues within 4Å: Chain A: T.357, D.359, A.360 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.357, A:D.359, A:A.360 EDO.14: 6 residues within 4Å: Chain A: Q.634, A.798, Q.801, I.849, K.853 Chain B: A.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.634, A:Q.801 Water bridges: A:A.798 EDO.15: 3 residues within 4Å: Chain A: A.805, Y.806, A.848 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.847

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

FE2.16: 4 residues within 4Å: Chain A: R.618, H.719, D.721, H.771 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.719, A:D.721, A:D.721, A:H.771, H2O.15

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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