SMTL ID : 3r5x.2 (1 other biounit)

Crystal Structure of D-alanine--D-Alanine Ligase from Bacillus anthracis complexed with ATP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: R.249, D.251, E.263, N.265 Ligands: ATP.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.251, A:E.263, H2O.5 CA.3: 1 residues within 4Å: Chain A: E.111 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.111, A:E.111, H2O.6 CA.5: 3 residues within 4Å: Chain B: D.251, E.263 Ligands: ATP.6 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.251, B:E.263, H2O.13 CA.7: 3 residues within 4Å: Chain B: E.203, D.206, Y.211 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.203, B:D.206, B:Y.211, H2O.13, H2O.13

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 16 residues within 4Å: Chain A: K.66, K.98, P.113, V.137, K.139, V.149, E.175, K.176, Y.177, I.178, E.182, M.253, M.262, E.263, N.265 Ligands: CA.1 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:K.139, A:E.175, A:E.175, A:I.178, A:E.182 Water bridges: A:E.69, A:E.69, A:E.263, A:N.265 Salt bridges: A:K.66, A:K.98, A:K.98, A:K.98, A:K.139 ATP.6: 14 residues within 4Å: Chain B: K.98, V.137, K.139, V.149, E.175, K.176, Y.177, I.178, E.182, M.253, M.262, E.263, N.265 Ligands: CA.5 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:K.139, B:E.175, B:E.175, B:I.178, B:E.182, B:E.263 Water bridges: B:E.69, B:E.69, B:E.69, B:K.98, B:K.98, B:K.98, B:K.98, B:K.98, B:G.144, B:G.144, B:E.263, B:E.263 Salt bridges: B:K.98, B:K.98, B:K.98, B:K.139

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 2 residues within 4Å: Chain A: R.302, E.305 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:R.302, A:E.305, H2O.6, H2O.6, H2O.6

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 5 residues within 4Å: Chain B: E.78, G.81, R.302, E.305, F.307 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.78, B:K.303, B:F.307

1 x ACY: ACETIC ACID(Non-functional Binders)

ACY.9: 2 residues within 4Å: Chain B: E.111, D.114 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal Structure of D-alanine--D-Alanine Ligase from Bacillus anthracis complexed with ATP. To be Published

Release Date

2011-04-06

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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