SMTL ID : 3qmn.5 (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

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 2 residues within 4Å: Chain A: D.115 Ligands: COA.9 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.115, A:D.115, H2O.97, H2O.242 CA.2: 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.25, H2O.165 CA.7: 2 residues within 4Å: Chain B: D.115 Ligands: COA.5 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.115, B:D.115, H2O.206 CA.11: 3 residues within 4Å: Chain C: D.11, E.60 Ligands: COA.9 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.11, C:E.60, H2O.94, H2O.272

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

CL.3: 2 residues within 4Å: Chain A: F.51, K.54 Ligand excluded by PLIP

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

MPD.4: 5 residues within 4Å: Chain A: R.17, V.18, F.29, F.56 Ligands: COA.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.18, A:F.29, A:F.56, A:F.56 Hydrogen bonds: A:R.17, A:R.17 Water bridges: A:E.14 MPD.10: 7 residues within 4Å: Chain C: A.13, R.17, V.18, A.21, F.29, F.56 Ligands: COA.9 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:A.13, C:A.21, C:F.29, C:F.56 Hydrogen bonds: C:R.17

3 x COA: COENZYME A(Non-covalent)

COA.5: 22 residues within 4Å: Chain A: D.11, 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, MPD.4, CA.7 13 PLIP interactions: 4 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:D.115, A:E.60, A:E.60, A:K.64, A:G.67, A:I.70, A:I.70 Water bridges: B:K.54 Salt bridges: B:K.54, B:H.83, A:K.64 Hydrophobic interactions: A:I.70, A:I.70 COA.6: 19 residues within 4Å: Chain B: D.11, F.56, E.60, 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: MRD.8, A3P.12 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:K.64, B:G.67, B:I.70, C:S.114, C:D.115, C:D.115 Salt bridges: B:K.64, C:K.54, C:H.83 Water bridges: C:K.54 COA.9: 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, F.56, E.60, S.63, K.64, G.67, T.68, G.69, I.70 Ligands: CA.1, MPD.10, CA.11 15 PLIP interactions: 9 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:I.70, C:I.70 Hydrogen bonds: C:K.64, C:G.67, C:I.70, C:I.70, A:S.114, A:D.115 Water bridges: C:E.60, C:T.68, A:K.54, A:R.55 Salt bridges: C:K.64, A:K.54, A:H.83

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

MRD.8: 6 residues within 4Å: Chain B: E.14, R.17, V.18, A.21, F.29 Ligands: COA.6 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.21, B:F.29 Hydrogen bonds: B:E.14

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

A3P.12: 13 residues within 4Å: Chain B: K.64, G.67, T.68, G.69 Chain C: K.54, H.83, L.86, G.87, K.88, P.89, I.113, D.115 Ligands: COA.6 10 PLIP interactions: 2 interactions with chain B, 8 interactions with chain C Hydrogen bonds: B:K.64, B:G.67 Water bridges: C:K.54, C:K.54, C:D.115, C:D.115, C:D.115 Salt bridges: C:K.54, C:K.54, C:H.83

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
M

B
N

C
O

Holo-[acyl-carrier-protein] synthase

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