SMTL ID : 3qmn.4 (7 other biounits)

Crystal Structure of 4'-Phosphopantetheinyl Transferase AcpS from Vibrio cholerae O1 biovar eltor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-trimer

Ligands

3 x COA: COENZYME A(Non-covalent)

COA.1: 22 residues within 4Å: Chain A: K.54, H.83, L.86, G.87, K.88, P.89, I.113, S.114, D.115 Chain C: D.11, I.33, E.60, S.63, K.64, G.67, T.68, G.69, I.70, F.76 Ligands: CA.4, CA.12, MRD.15 16 PLIP interactions: 9 interactions with chain A, 7 interactions with chain C Hydrogen bonds: A:S.114, A:D.115, C:K.64, C:G.67, C:I.70, C:I.70 Water bridges: A:K.54, A:K.54, A:R.55, A:R.55, A:R.55 Salt bridges: A:K.54, A:H.83, C:K.64 Hydrophobic interactions: C:I.70, C:I.70 COA.7: 22 residues within 4Å: Chain A: D.11, F.29, F.56, E.60, S.63, K.64, G.67, T.68, G.69, I.70, F.76 Chain B: K.54, H.83, L.86, G.87, K.88, P.89, I.113, S.114, D.115 Ligands: CA.2, CA.5 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:D.11, A:K.64, A:G.67, A:I.70, B:D.115 Salt bridges: A:K.64, B:K.54, B:H.83 Water bridges: B:R.55 COA.11: 23 residues within 4Å: Chain B: D.11, R.32, F.56, E.60, S.63, K.64, G.67, T.68, G.69, I.70, F.76 Chain C: K.54, H.83, L.86, G.87, K.88, P.89, I.113, S.114, D.115 Ligands: CA.8, MRD.10, CA.13 15 PLIP interactions: 8 interactions with chain B, 7 interactions with chain C Hydrogen bonds: B:R.32, B:R.32, B:K.64, B:G.67, B:I.70, B:I.70, C:S.114, C:D.115 Water bridges: B:T.68, C:K.54, C:R.55, C:D.115 Salt bridges: B:K.64, C:K.54, C:H.83

6 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.11, E.60 Chain B: S.114 Ligands: COA.7 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.11, A:E.60, H2O.19, H2O.149, H2O.184 CA.4: 2 residues within 4Å: Chain A: D.115 Ligands: COA.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.115, A:D.115, H2O.56, H2O.66 CA.5: 3 residues within 4Å: Chain B: D.115 Ligands: ACT.6, COA.7 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.115, B:D.115, H2O.176, H2O.234 CA.8: 3 residues within 4Å: Chain B: D.11, E.60 Ligands: COA.11 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.11, B:E.60, H2O.162, H2O.178 CA.12: 3 residues within 4Å: Chain C: D.11, E.60 Ligands: COA.1 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.11, C:E.60, H2O.22, H2O.272 CA.13: 2 residues within 4Å: Chain C: D.115 Ligands: COA.11 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.115, C:D.115, H2O.333, H2O.362

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

CL.3: 3 residues within 4Å: Chain A: Q.47, F.51, K.54 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain C: Q.47, F.51, K.54 Ligand excluded by PLIP

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 6 residues within 4Å: Chain A: R.17 Chain B: R.50, D.115, E.116, R.117 Ligands: CA.5 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:R.17 Water bridges: B:R.50, B:D.115, B:R.117 Salt bridges: B:R.50 ACT.9: 2 residues within 4Å: Chain B: E.19, R.50 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.50

2 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.10: 7 residues within 4Å: Chain B: A.13, R.17, V.18, A.21, F.29, F.56 Ligands: COA.11 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:A.13, B:V.18, B:A.21, B:F.29, B:F.56, B:F.56 Hydrogen bonds: B:R.17, B:R.17 MRD.15: 7 residues within 4Å: Chain C: A.13, R.17, V.18, A.21, F.29, F.56 Ligands: COA.1 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:A.13, C:V.18, C:A.21, C:F.29, C:F.56, C:F.56 Hydrogen bonds: C:R.17 Water bridges: C:R.17

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

2011-03-02

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
J

B
K

C
L

Holo-[acyl-carrier-protein] synthase

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