SMTL ID : 3q1k.1 (1 other biounit)

The Crystal Structure of the D-alanyl-alanine Synthetase A from Salmonella enterica Typhimurium Complexed with ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 17 residues within 4Å: Chain A: K.144, A.159, F.186, K.188, G.193, S.194, S.195, E.224, Q.225, G.226, I.227, E.231, L.252, F.307, N.317, E.318 Ligands: MG.3 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:K.188, A:Q.192, A:G.193, A:S.194, A:S.195, A:E.224, A:E.224, A:I.227, A:E.231, A:N.317, A:E.318 Water bridges: A:K.144, A:K.148, A:E.318 Salt bridges: A:K.144, A:K.144, A:K.188 pi-Stacking: A:F.186, A:F.186 ADP.5: 17 residues within 4Å: Chain B: K.144, F.186, K.188, Q.192, G.193, S.194, S.195, V.198, E.224, Q.225, G.226, I.227, E.231, F.307, N.317, E.318 Ligands: MG.6 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:K.188, B:S.194, B:S.195, B:E.224, B:I.227, B:E.231, B:N.317, B:E.318, B:E.318, B:E.318 Salt bridges: B:K.144, B:K.144, B:K.188 pi-Stacking: B:F.186, B:F.186

4 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 6 residues within 4Å: Chain A: P.129, F.130, A.353, R.356, H.357, N.360 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.130, A:N.360 FMT.7: 4 residues within 4Å: Chain B: L.237, G.238, Q.243, R.348 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.237, B:Q.243, B:R.348 Water bridges: B:N.239 FMT.8: 8 residues within 4Å: Chain B: H.88, Q.89, L.90, L.99, P.100, T.101, V.102, L.128 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.89, B:L.90, B:V.102, B:V.102 FMT.9: 5 residues within 4Å: Chain B: N.239, D.240, G.297, C.298, A.299 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.239

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: E.318 Ligands: ADP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.318, H2O.5, H2O.5, H2O.5 MG.6: 3 residues within 4Å: Chain B: D.305, E.318 Ligands: ADP.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.318

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: N.239, D.240, G.297, C.298, A.299, R.356 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.240, A:G.297, A:R.356 GOL.11: 8 residues within 4Å: Chain B: C.141, M.142, K.144, A.190, Q.192, E.318, I.319, N.320 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:C.141, B:Q.192, B:Q.192, B:E.318, B:N.320 Water bridges: B:E.115, B:I.319

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.10: 4 residues within 4Å: Chain B: R.303, G.324, S.329, M.330 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.303, B:R.303 Salt bridges: B:R.303

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, R. et al., The Crystal Structure of the D-alanyl-alanine Synthetase A from Salmonella enterica Typhimurium Complexed with ADP. To be Published

Release Date

2011-01-12

Peptides

D-alanine--D-alanine ligase A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D-alanine--D-alanine ligase A

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