SMTL ID : 1iov.1

COMPLEX OF D-ALA:D-ALA LIGASE WITH ADP AND A PHOSPHORYL PHOSPHONATE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: K.215, D.257, E.270 Ligands: ADP.4, POB.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.257, A:E.270 MG.2: 6 residues within 4Å: Chain A: E.148, G.149, E.270, N.272 Ligands: ADP.4, POB.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.270, A:E.270, H2O.6 MG.3: 5 residues within 4Å: Chain A: S.94, M.95, E.270, A.271, N.272 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.94, A:A.271

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

ADP.4: 23 residues within 4Å: Chain A: K.97, I.142, K.144, E.148, G.149, S.150, S.151, M.154, E.180, K.181, W.182, L.183, E.187, F.209, Y.210, K.215, D.257, M.259, L.269, E.270 Ligands: MG.1, MG.2, POB.5 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:K.144, A:S.150, A:S.151, A:E.180, A:E.180, A:L.183, A:E.187, A:Y.210 Water bridges: A:V.152 Salt bridges: A:K.97, A:K.97, A:K.144, A:K.215, A:K.215

1 x POB: 2-[(1-AMINO-ETHYL)-PHOSPHATE-PHOSPHINOYLOXY]-BUTYRIC ACID(Non-covalent)

POB.5: 19 residues within 4Å: Chain A: E.15, V.18, H.63, G.149, S.150, Y.210, K.215, Y.216, R.255, D.257, E.270, N.272, P.275, G.276, S.281, L.282 Ligands: MG.1, MG.2, ADP.4 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:V.18, A:K.215, A:K.215, A:L.282 Hydrogen bonds: A:S.150, A:Y.216, A:Y.216, A:R.255, A:R.255, A:N.272, A:G.276, A:L.282 Water bridges: A:V.283 Salt bridges: A:K.215, A:R.255, A:R.255

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fan, C. et al., D-alanine:D-alanine ligase: phosphonate and phosphinate intermediates with wild type and the Y216F mutant. Biochemistry (1997)

Release Date

1997-02-12

Peptides

D-ALA\:D-ALA LIGASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D-ALA\:D-ALA LIGASE

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