SMTL ID : 6lna.2 (1 other biounit)

YdiU complex with AMPNPP and Mn2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: R.177, N.247, D.256 Ligands: ANP.3 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.256, H2O.5 MN.2: 3 residues within 4Å: Chain A: R.87, D.256 Ligands: ANP.3 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.256, A:D.256, H2O.14, H2O.19, H2O.21

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

ANP.3: 21 residues within 4Å: Chain A: Y.71, Q.75, L.83, G.84, G.86, R.87, K.107, S.115, R.116, G.118, D.119, G.120, R.121, R.159, R.170, R.177, D.246, N.247, D.256 Ligands: MN.1, MN.2 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:Y.71, A:G.86, A:R.87, A:R.87, A:R.87, A:K.107, A:R.116, A:D.119, A:D.119, A:D.119, A:G.120, A:R.121, A:R.159, A:R.170, A:R.170, A:R.177, A:R.177, A:N.247 Water bridges: A:Y.71, A:Y.71, A:Q.75, A:Q.75, A:R.159

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 1 residues within 4Å: Chain A: D.265 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.265, H2O.5, H2O.16, H2O.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Y. et al., The YdiU Domain Modulates Bacterial Stress Signaling through Mn 2+ -Dependent UMPylation. Cell Rep (2020)

Release Date

2020-12-30

Peptides

Protein adenylyltransferase SelO: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Protein adenylyltransferase SelO

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