SMTL ID : 2zdh.2 (1 other biounit)

Crystal structure of D-Alanine:D-Alanine Ligase with ADP and D-Alanine from Thermus thermophius HB8

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.270, E.282 Ligands: ADP.3 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.282, H2O.6, H2O.6, H2O.6 MG.2: 2 residues within 4Å: Chain A: E.282, N.284 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:E.282, H2O.6, H2O.6, H2O.6, H2O.6, H2O.6 MG.4: 3 residues within 4Å: Chain B: D.270, E.282 Ligands: ADP.5 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.282, H2O.11, H2O.11, H2O.11

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

ADP.3: 16 residues within 4Å: Chain A: K.116, F.151, K.153, G.158, S.159, S.160, I.163, E.189, K.190, A.191, L.192, E.197, F.272, N.281, E.282 Ligands: MG.1 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:K.153, A:S.160, A:E.189, A:L.192, A:E.197, A:N.281, A:E.282 Water bridges: A:S.159, A:S.160, A:Y.218, A:E.282 Salt bridges: A:K.116, A:K.153 pi-Stacking: A:F.151, A:F.151 ADP.5: 21 residues within 4Å: Chain B: K.116, V.131, F.151, K.153, T.157, G.158, S.159, S.160, I.163, E.189, K.190, A.191, L.192, E.197, Y.218, F.222, Y.223, F.272, N.281, E.282 Ligands: MG.4 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:K.153, B:T.157, B:S.159, B:S.160, B:E.189, B:L.192, B:E.197, B:Y.223, B:N.281, B:E.282 Water bridges: B:E.197, B:Y.218, B:E.282, B:E.282, B:E.282 Salt bridges: B:K.116, B:K.116, B:K.153 pi-Stacking: B:F.151, B:F.151

1 x DAL: D-ALANINE(Non-covalent)

DAL.6: 8 residues within 4Å: Chain B: E.13, V.16, H.82, K.228, Y.229, R.268, N.284, G.288 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:V.16 Hydrogen bonds: B:E.13, B:N.284, B:G.288 Water bridges: B:S.159, B:S.159, B:S.159, B:S.159, B:R.268 Salt bridges: B:K.228, B:R.268

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kitamura, Y. et al., Crystal structure of D-Alanine:D-Alanine Ligase with ADP and D-Alanine from Thermus thermophius HB8. To be Published

Release Date

2008-05-27

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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