SMTL ID : 3hyk.1

2.31 Angstrom resolution crystal structure of a holo-(acyl-carrier-protein) synthase from Bacillus anthracis str. Ames in complex with CoA (3',5'-ADP)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

homo-trimer

Ligands

9 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 2 residues within 4Å: Chain A: H.106 Ligands: A3P.5 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.106, A:H.106, H2O.3, H2O.3, H2O.6 MG.2: 4 residues within 4Å: Chain A: D.11, E.61 Chain C: S.105 Ligands: A3P.21 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.11, A:E.61, H2O.2, H2O.3, H2O.9 MG.4: 2 residues within 4Å: Ligands: A3P.6, A3P.21 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Ligands: A3P.5, A3P.14 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain A: S.105 Chain B: D.11, E.61 Ligands: A3P.5 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.11, B:E.61, H2O.3, H2O.6, H2O.6 MG.10: 3 residues within 4Å: Chain B: H.106 Ligands: A3P.13, A3P.20 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.106, B:H.106, H2O.6, H2O.6, H2O.9 MG.15: 4 residues within 4Å: Chain B: S.105 Chain C: D.11, E.61 Ligands: A3P.13 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.11, C:E.61, H2O.6, H2O.9, H2O.9 MG.16: 2 residues within 4Å: Chain C: H.106 Ligands: A3P.21 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:H.106, C:H.106, H2O.2, H2O.9, H2O.9 MG.18: 2 residues within 4Å: Ligands: A3P.13, A3P.20 No protein-ligand interaction detected (PLIP)

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

CL.3: 3 residues within 4Å: Chain A: E.61, G.70, I.71 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: E.61, G.70, I.71 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain B: E.51, F.52, G.55, R.56 Ligands: A3P.13 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain A: S.107 Chain B: I.13, E.14, R.17 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain C: E.61, G.70, I.71 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain B: S.107 Chain C: I.13, E.14, R.17 Ligand excluded by PLIP

6 x A3P: ADENOSINE-3'-5'-DIPHOSPHATE(Non-covalent)

A3P.5: 20 residues within 4Å: Chain A: R.48, R.56, N.84, R.87, G.88, K.89, P.90, I.104, S.105, H.106 Chain B: D.11, E.61, K.65, G.68, T.69, G.70 Ligands: MG.1, MG.7, MG.8, A3P.14 19 PLIP interactions: 5 interactions with chain B, 14 interactions with chain A Hydrogen bonds: B:K.65, B:G.68, A:N.84, A:N.84, A:H.106 Water bridges: B:E.61, B:E.61, A:R.56, A:R.56, A:S.105, A:H.106, A:H.106, A:H.106, A:H.106 Salt bridges: B:K.65, A:R.48, A:R.56, A:H.106, A:H.106 A3P.6: 5 residues within 4Å: Chain A: R.17, M.21, R.31 Ligands: MG.4, A3P.21 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.17, A:R.17, A:R.31 Water bridges: A:R.31 A3P.13: 21 residues within 4Å: Chain B: R.48, R.56, N.84, R.87, G.88, K.89, P.90, I.104, S.105, H.106 Chain C: D.11, E.61, K.65, G.68, T.69, G.70 Ligands: MG.10, CL.11, MG.15, MG.18, A3P.20 15 PLIP interactions: 2 interactions with chain C, 13 interactions with chain B Hydrogen bonds: C:K.65, B:N.84, B:N.84, B:R.87, B:H.106, B:H.106 Salt bridges: C:K.65, B:R.48, B:R.56, B:H.106, B:H.106 Water bridges: B:K.89, B:H.106, B:H.106, B:H.106 A3P.14: 4 residues within 4Å: Chain B: R.17, R.31 Ligands: A3P.5, MG.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.17, B:R.31 Water bridges: B:R.31 A3P.20: 6 residues within 4Å: Chain C: R.17, M.21, R.31 Ligands: MG.10, A3P.13, MG.18 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:R.17, C:R.31 Water bridges: C:R.31, B:H.106 A3P.21: 20 residues within 4Å: Chain A: D.11, E.61, K.65, G.68, T.69, G.70 Chain C: R.48, R.56, N.84, R.87, G.88, K.89, P.90, I.104, S.105, H.106 Ligands: MG.2, MG.4, A3P.6, MG.16 16 PLIP interactions: 12 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:N.84, C:N.84, C:H.106, C:H.106, A:D.11, A:K.65, A:G.68 Water bridges: C:R.56, C:R.56, C:H.106, C:H.106 Salt bridges: C:R.48, C:R.56, C:H.106, C:H.106, A:K.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Halavaty, A.S. et al., Structural characterization and comparison of three acyl-carrier-protein synthases from pathogenic bacteria. Acta Crystallogr.,Sect.D (2012)

Release Date

2009-06-30

Peptides

Holo-[acyl-carrier-protein] synthase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Holo-[acyl-carrier-protein] synthase