SMTL ID : 3qmn.7 (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, R.55, H.83, L.86, G.87, K.88, P.89, I.113, S.114, D.115 Chain C: D.11, E.60, S.63, K.64, G.67, T.68, G.69, I.70, F.76 Ligands: CA.3, MPD.11, CA.13 13 PLIP interactions: 9 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:S.114, A:D.115, A:D.115, C:K.64, C:G.67, C:I.70 Water bridges: A:R.55, A:D.115, A:D.115 Salt bridges: A:K.54, A:R.55, A:H.83, C:K.64 COA.5: 23 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: MPD.2, CA.4, CA.6 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrogen bonds: 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:K.54 COA.12: 21 residues within 4Å: Chain B: D.11, F.29, F.56, E.60, S.63, K.64, G.67, T.68, G.69, I.70 Chain C: K.54, H.83, L.86, G.87, K.88, P.89, I.113, S.114, D.115 Ligands: CA.7, CA.14 14 PLIP interactions: 7 interactions with chain C, 7 interactions with chain B Hydrogen bonds: C:S.114, C:D.115, B:K.64, B:G.67, B:I.70, B:I.70 Water bridges: C:R.55, C:R.55, C:R.55 Salt bridges: C:K.54, C:H.83, B:K.64 Hydrophobic interactions: B:I.70, B:I.70

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 4 residues within 4Å: Chain A: R.17, F.56 Ligands: COA.5, ACT.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.56 Hydrogen bonds: A:R.17 MPD.11: 7 residues within 4Å: Chain C: A.13, R.17, V.18, A.21, F.29, F.56 Ligands: COA.1 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:A.13, C:V.18, C:A.21, C:F.29, C:F.56 Water bridges: C:R.17

6 x CA: CALCIUM ION(Non-covalent)

CA.3: 2 residues within 4Å: Chain A: D.115 Ligands: COA.1 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.115, A:D.115, H2O.91, H2O.92, H2O.96 CA.4: 3 residues within 4Å: Chain A: D.11, E.60 Ligands: COA.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.11, A:E.60, H2O.21, H2O.38 CA.6: 3 residues within 4Å: Chain B: D.115 Ligands: COA.5, ACT.8 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.115, B:D.115, H2O.114, H2O.148 CA.7: 4 residues within 4Å: Chain B: D.11, E.60 Chain C: S.114 Ligands: COA.12 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.11, B:E.60, H2O.122, H2O.171 CA.13: 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.228, H2O.252 CA.14: 2 residues within 4Å: Chain C: D.115 Ligands: COA.12 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.115, C:D.115, H2O.196

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

ACT.8: 7 residues within 4Å: Chain A: R.17 Chain B: R.50, D.115, E.116, R.117 Ligands: MPD.2, CA.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.115 Water bridges: B:R.50 Salt bridges: B:R.50

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

MRD.9: 6 residues within 4Å: Chain B: A.13, E.14, R.17, V.18, A.21, F.56 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.13, B:V.18, B:A.21, B:F.56, B:F.56 Hydrogen bonds: B:R.17, B:R.17

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

CL.10: 3 residues within 4Å: Chain B: Q.47, F.51, K.54 Ligand excluded by PLIP

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
S

B
T

C
U

Holo-[acyl-carrier-protein] synthase

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