SMTL ID : 6u1i.2 (1 other biounit)

Thermus thermophilus D-alanine-D-alanine ligase in complex with ADP, phosphorylated D-cycloserine, Mg2+ and K+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: K.230, D.272, E.284 Ligands: MG.2, ADP.4, DS0.5 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.284, H2O.1, H2O.1 MG.2: 7 residues within 4Å: Chain A: K.118, E.284, N.286 Ligands: MG.1, K.3, ADP.4, DS0.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.284, A:E.284, H2O.2

1 x K: POTASSIUM ION(Non-covalent)

K.3: 6 residues within 4Å: Chain A: C.115, M.116, E.284, L.285, N.286 Ligands: MG.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.115, A:E.284, A:L.285, H2O.2, H2O.3

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.4: 24 residues within 4Å: Chain A: K.118, V.133, F.153, K.155, T.159, G.160, S.161, S.162, I.165, E.191, K.192, A.193, L.194, E.199, Y.220, F.224, Y.225, K.230, F.274, N.283, E.284 Ligands: MG.1, MG.2, DS0.5 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:K.155, A:G.160, A:S.161, A:S.162, A:E.191, A:E.191, A:L.194, A:E.199, A:Y.220, A:Y.225, A:N.283, A:E.284 Water bridges: A:K.230, A:R.270 Salt bridges: A:K.118, A:K.118, A:K.155, A:K.230, A:K.230 pi-Stacking: A:F.153, A:F.153

1 x DS0: [(4R)-4-azanyl-4,5-dihydro-1,2-oxazol-3-yl] dihydrogen phosphate(Non-covalent)

DS0.5: 16 residues within 4Å: Chain A: E.15, H.84, G.160, S.161, K.230, Y.231, R.270, D.272, E.284, N.286, I.288, P.289, G.290 Ligands: MG.1, MG.2, ADP.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.161, A:R.270, A:D.272, A:N.286, A:G.290 Water bridges: A:K.230 Salt bridges: A:K.230, A:R.270

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pederick, J.L. et al., d-Alanine-d-alanine ligase as a model for the activation of ATP-grasp enzymes by monovalent cations. J.Biol.Chem. (2020)

Release Date

2020-05-06

Peptides

D-alanine--D-alanine ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

D-alanine--D-alanine ligase

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