SMTL ID : 8h68.1

Crystal structure of Caenorhabditis elegans NMAD-1 in complex with NOG and Mg(II)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x GLC- GLC- GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose

GLC-GLC-GLC-GLC.1: 23 residues within 4Å: Chain A: N.14, D.16, K.17, K.44, E.46, E.47, W.64, A.65, D.67, R.68, E.113, E.155, P.156, Y.157, F.158, W.232, M.332, W.342, Y.343, R.346, K.377, D.554 Ligands: PEG.7 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.44, A:K.44, A:E.46, A:K.377 Water bridges: A:K.44, A:R.346

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 3 residues within 4Å: Chain A: E.40, H.41, P.42 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.41, A:H.41

1 x GLY: GLYCINE(Non-covalent)

GLY.3: 5 residues within 4Å: Chain A: S.272, P.273, N.274, K.275, E.276 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:K.275, A:E.276, G.3, G.3 Salt bridges: A:K.275

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

OGA.4: 14 residues within 4Å: Chain A: L.514, Y.516, I.524, H.527, D.529, S.540, M.549, H.582, V.584, R.593, A.595, T.597, R.599 Ligands: MG.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.540 Water bridges: A:R.599 Salt bridges: A:H.582, A:R.593, A:R.599

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain A: H.527, D.529, H.582 Ligands: OGA.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.527, A:D.529, A:H.582, H2O.3

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.6: 9 residues within 4Å: Chain A: N.351, R.356, Q.357, D.365, N.369, V.379, N.380, Y.381, K.382 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.356, A:N.369 Water bridges: A:N.351, A:K.382

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 8 residues within 4Å: Chain A: N.14, D.16, K.44, L.45, E.46, W.64 Ligands: GLC-GLC-GLC-GLC.1, GLC-GLC-GLC-GLC.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.14, A:K.44, A:L.45, A:E.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, Y. et al., Caenorhabditis elegans NMAD-1 functions as a demethylase for actin. J Mol Cell Biol (2023)

Release Date

2023-02-22

Peptides

Maltose/maltodextrin-binding periplasmic protein,DNA N6-methyl adenine demethylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Maltose/maltodextrin-binding periplasmic protein,DNA N6-methyl adenine demethylase