SMTL ID : 2h7x.2 (1 other biounit)

Pikromycin Thioesterase adduct with reduced triketide affinity label

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: A.58, Q.62, R.236 Chain B: R.45 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.62 Water bridges: A:A.141, A:R.236 Salt bridges: A:R.236, B:R.45 SO4.3: 1 residues within 4Å: Chain A: R.269 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.269 SO4.5: 4 residues within 4Å: Chain A: R.45 Chain B: A.58, Q.62, R.236 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.62 Water bridges: B:S.57, B:A.58, B:R.236, B:R.236, B:R.236, A:R.45 Salt bridges: B:R.236, A:R.45 SO4.9: 4 residues within 4Å: Chain C: A.58, Q.62, R.236 Chain D: R.45 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Q.62 Water bridges: C:A.141, C:R.236 Salt bridges: C:R.236, D:R.45 SO4.11: 1 residues within 4Å: Chain C: R.269 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.269 SO4.13: 4 residues within 4Å: Chain C: R.45 Chain D: A.58, Q.62, R.236 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:Q.62 Water bridges: D:S.57, D:A.58, D:R.236, D:R.236, D:R.236, C:R.45 Salt bridges: D:R.236, C:R.45

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: H.275, D.277 Chain C: H.275, D.277 Ligands: MG.10 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: A:D.277, C:D.277, H2O.2, H2O.20 MG.10: 5 residues within 4Å: Chain A: H.275, D.277 Chain C: H.275, D.277 Ligands: MG.2 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: A:D.277, C:D.277, H2O.2, H2O.20

4 x PSX: [(2S,3R,4S)-2,4-DIHYDROXY-3-METHYLHEXYL]PHOSPHONIC ACID(Covalent)

PSX.4: 8 residues within 4Å: Chain A: T.98, S.169, G.170, L.173, I.207, A.238, L.241, H.289 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.173, A:I.207, A:L.241 Hydrogen bonds: A:G.170 Water bridges: A:T.98, A:S.169, A:S.169, A:A.238 PSX.6: 8 residues within 4Å: Chain B: S.169, G.170, L.173, I.207, L.214, A.238, L.241, H.289 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.173, B:I.207, B:L.214, B:L.241 Hydrogen bonds: B:G.170 Water bridges: B:A.238 PSX.12: 8 residues within 4Å: Chain C: T.98, S.169, G.170, L.173, I.207, A.238, L.241, H.289 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.173, C:I.207, C:L.241 Hydrogen bonds: C:G.170 Water bridges: C:T.98, C:S.169, C:S.169, C:A.238 PSX.14: 8 residues within 4Å: Chain D: S.169, G.170, L.173, I.207, L.214, A.238, L.241, H.289 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:L.173, D:I.207, D:L.214, D:L.241 Hydrogen bonds: D:G.170 Water bridges: D:A.238

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.7: 5 residues within 4Å: Chain B: P.200, H.203, R.248, W.276, D.277 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.248, B:R.248, B:D.277 Salt bridges: B:D.277 pi-Cation interactions: B:W.276, B:W.276 DMS.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) DMS.15: 5 residues within 4Å: Chain D: P.200, H.203, R.248, W.276, D.277 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.248, D:R.248, D:D.277 Salt bridges: D:D.277 pi-Cation interactions: D:W.276, D:W.276 DMS.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Giraldes, J.W. et al., Structural and Mechanistic Insights of Polyketide Macrolactonization from Polyketide-based Affinity Labels. NAT.CHEM.BIOL. (2006)

Release Date

2006-09-19

Peptides

Type I polyketide synthase PikAIV: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Type I polyketide synthase PikAIV

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