SMTL ID : 4q86.2 (3 other biounits)

YcaO with AMP Bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 17 residues within 4Å: Chain A: L.13, S.16, F.20, K.61, A.70, S.71, G.74, E.75, E.78, S.184, A.185, G.186, N.187, E.191, Q.195, R.286 Ligands: MG.4 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.16, A:E.78, A:A.185, A:N.187, A:Q.195 Water bridges: A:L.13, A:R.286, A:R.286, A:R.286, A:E.290 Salt bridges: A:K.61, A:R.286 AMP.5: 18 residues within 4Å: Chain B: K.9, L.13, S.16, F.20, K.61, A.70, S.71, G.74, E.75, E.78, S.184, A.185, G.186, N.187, E.191, Q.195, R.286 Ligands: MG.7 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:K.9, B:S.16, B:S.16, B:E.78, B:E.78, B:A.185, B:N.187, B:Q.195 Water bridges: B:K.9, B:S.71, B:R.286, B:R.286, B:R.286 Salt bridges: B:K.61, B:R.286 pi-Cation interactions: B:K.9

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: S.215, L.216, Y.247, L.334, F.335, K.336 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:S.215, A:L.216, A:L.334, A:K.336 MG.3: 3 residues within 4Å: Chain A: E.78, Q.195, E.199 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.199, H2O.2, H2O.4, H2O.9, H2O.9 MG.4: 2 residues within 4Å: Chain A: E.75 Ligands: AMP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.75, H2O.2, H2O.6, H2O.9, H2O.9 MG.6: 6 residues within 4Å: Chain B: S.215, L.216, Y.247, L.334, F.335, K.336 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:S.215, B:L.216, B:L.334, B:K.336 MG.7: 2 residues within 4Å: Chain B: E.75 Ligands: AMP.5 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.75, H2O.10, H2O.14, H2O.17, H2O.19 MG.8: 2 residues within 4Å: Chain B: E.78, E.199 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.199, H2O.14, H2O.19, H2O.19, H2O.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dunbar, K.L. et al., Discovery of a new ATP-binding motif involved in peptidic azoline biosynthesis. Nat.Chem.Biol. (2014)

Release Date

2014-08-13

Peptides

Ribosomal protein S12 methylthiotransferase accessory factor YcaO: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Ribosomal protein S12 methylthiotransferase accessory factor YcaO

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