SMTL ID : 7r78.1

cryo-EM structure of DNMT5 quaternary complex with hemimethylated DNA, AMP-PNP and SAH

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 13 residues within 4Å: Chain A: C.324, S.325, G.326, E.358, I.359, E.360, K.363, D.379, V.380, N.703, A.704, M.705 Chain C: C.6 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:C.324, A:G.326, A:I.359, A:K.363, A:D.379, A:V.380, A:N.703, A:M.705

5 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.788, C.790, C.811, C.814 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.788, A:C.790, A:C.811 ZN.3: 4 residues within 4Å: Chain A: C.803, C.806, H.820, C.1036 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.803, A:C.806, A:H.820, A:C.1036 ZN.4: 4 residues within 4Å: Chain A: C.1171, C.1242, C.1245, H.1319 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.1171, A:C.1242, A:C.1245 ZN.5: 4 residues within 4Å: Chain A: C.2052, A.2074, C.2075, C.2078 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.2052 ZN.6: 4 residues within 4Å: Chain A: C.2070, H.2072, C.2088, C.2094 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.2070, A:C.2088, A:C.2094

1 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.7: 20 residues within 4Å: Chain A: P.1375, L.1376, R.1377, Q.1380, V.1436, G.1437, Y.1438, G.1439, K.1440, T.1441, V.1442, Q.1481, E.1485, R.1488, F.1489, N.2205, R.2236, R.2239, Y.2240 Ligands: MG.8 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:P.1375, A:R.1377, A:Q.1380, A:G.1437, A:K.1440, A:T.1441, A:T.1441, A:Q.1481, A:E.1485, A:R.1488, A:R.1488, A:N.2205, A:N.2205, A:R.2236 Salt bridges: A:R.2239 pi-Stacking: A:F.1489

1 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 2 residues within 4Å: Chain A: E.1697 Ligands: ANP.7 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.1697

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, J. et al., Structural insights into DNMT5-mediated ATP-dependent high-fidelity epigenome maintenance. Mol.Cell (2022)

Release Date

2022-02-23

Peptides

DNA repair protein Rad8: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA repair protein Rad8

Related Entries With Identical Sequence