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

Crystal structure of L-amino acid ligase from Bacillus licheniformis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

ADP.1: 18 residues within 4Å: Chain A: K.113, V.149, K.151, G.155, V.161, E.198, Q.199, F.200, I.201, E.205, F.233, E.273, R.275, I.285, E.286 Ligands: CA.2, CA.3, CA.4 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:K.151, A:G.155, A:E.198, A:I.201, A:E.205, A:E.273, A:R.275 Water bridges: A:V.161, A:E.235 Salt bridges: A:K.113, A:K.113, A:K.151

5 x CA: CALCIUM ION(Non-covalent)

CA.2: 2 residues within 4Å: Chain A: E.205 Ligands: ADP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.205, H2O.6, H2O.7, H2O.9, H2O.11 CA.3: 4 residues within 4Å: Chain A: E.273, E.286 Ligands: ADP.1, CA.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.273, A:E.273, A:E.286, H2O.6, H2O.8 CA.4: 4 residues within 4Å: Chain A: E.84, E.286 Ligands: ADP.1, CA.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.84, A:E.286, H2O.6, H2O.8 CA.5: 1 residues within 4Å: Chain A: Q.214 No protein-ligand interaction detected (PLIP) CA.6: 3 residues within 4Å: Chain A: R.163, D.165, E.169 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.165, A:E.169, A:E.169, H2O.13

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 4 residues within 4Å: Chain A: C.12, Q.13, Y.35, N.36 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Suzuki, M. et al., The structure of L-amino-acid ligase from Bacillus licheniformis. Acta Crystallogr.,Sect.D (2012)

Release Date

2012-11-07

Peptides

L-amino acid ligase, BL00235: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

L-amino acid ligase, BL00235

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