SMTL ID : 3wo1.1

Crystal structure of Trp332Ala mutant YwfE, an L-amino acid ligase, with bound ADP-Mg-Ala

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 18 residues within 4Å: Chain A: K.140, I.178, K.180, L.184, A.185, S.186, S.187, E.228, E.229, F.230, L.231, Q.270, F.273, E.313, I.325, E.326 Ligands: MG.2, MG.3 13 PLIP interactions: 12 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:K.180, A:S.187, A:E.229, A:L.231, A:Q.270, A:E.313 Water bridges: A:K.315, A:E.326, A:E.326, A.4 Salt bridges: A:K.140, A:K.140, A:K.180 ADP.5: 18 residues within 4Å: Chain B: K.140, I.178, K.180, L.184, A.185, S.186, S.187, E.228, E.229, F.230, L.231, Q.270, F.273, E.313, I.325, E.326 Ligands: MG.6, MG.7 14 PLIP interactions: 13 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:K.180, B:S.187, B:E.228, B:E.229, B:L.231, B:Q.270, B:E.313 Water bridges: B:K.315, B:E.326, B:E.326, A.8 Salt bridges: B:K.140, B:K.140, B:K.180

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: E.313, E.326 Ligands: ADP.1, MG.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.313, A:E.326, H2O.4 MG.3: 4 residues within 4Å: Chain A: E.111, E.326 Ligands: ADP.1, MG.2 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain B: E.313, E.326 Ligands: ADP.5, MG.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.313, B:E.326, H2O.7 MG.7: 4 residues within 4Å: Chain B: E.111, E.326 Ligands: ADP.5, MG.6 No protein-ligand interaction detected (PLIP)

2 x ALA: ALANINE(Non-covalent)

ALA.4: 7 residues within 4Å: Chain A: E.275, H.311, E.313, R.330, A.332, G.333, M.336 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.275, A:G.333 Water bridges: A:R.330, A:R.330 Salt bridges: A:H.311, A:R.330 ALA.8: 7 residues within 4Å: Chain B: E.275, H.311, E.313, R.330, A.332, G.333, M.336 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.275, B:G.333 Water bridges: B:E.313, B:R.330, B:R.330 Salt bridges: B:H.311, B:R.330

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsuda, T. et al., Single Mutation Alters the Substrate Specificity of l-Amino Acid Ligase. Biochemistry (2014)

Release Date

2014-05-14

Peptides

Alanine-anticapsin ligase BacD: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Alanine-anticapsin ligase BacD