SMTL ID : 2h7y.2 (1 other biounit)

Pikromycin Thioesterase with covalent affinity label

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 1 residues within 4Å: Chain A: R.269 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.269 SO4.2: 4 residues within 4Å: Chain A: A.58, Q.62, R.236 Chain B: R.45 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:R.45, A:R.236 Hydrogen bonds: A:Q.62 SO4.5: 4 residues within 4Å: Chain A: R.45 Chain B: A.58, Q.62, R.236 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Q.62 Salt bridges: B:R.236, A:R.45 Water bridges: A:R.45, A:R.45 SO4.9: 1 residues within 4Å: Chain C: R.269 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.269 SO4.10: 4 residues within 4Å: Chain C: A.58, Q.62, R.236 Chain D: R.45 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Q.62 Salt bridges: C:R.236, D:R.45 SO4.13: 4 residues within 4Å: Chain C: R.45 Chain D: A.58, Q.62, R.236 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:Q.62 Salt bridges: D:R.236, C:R.45 Water bridges: C:R.45, C:R.45

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: H.275, D.277 Chain C: H.275, D.277, L.278 Ligands: MG.11 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:D.277, A:D.277, H2O.3, H2O.19 MG.11: 6 residues within 4Å: Chain A: H.275, D.277, L.278 Chain C: H.275, D.277 Ligands: MG.3 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:D.277, A:D.277, H2O.3, H2O.19

4 x PSK: [(3R,4S)-4-HYDROXY-3-METHYL-2-OXOHEXYL]PHOSPHONIC ACID(Covalent)

PSK.4: 9 residues within 4Å: Chain A: Y.46, T.98, S.169, G.170, L.173, I.207, A.238, L.241, H.289 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.173, A:I.207, A:L.241 Hydrogen bonds: A:G.170 Water bridges: A:Y.46, A:T.98, A:G.171 PSK.8: 7 residues within 4Å: Chain B: S.169, G.170, L.173, I.207, L.214, L.241, H.289 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.173, B:L.241 Hydrogen bonds: B:G.170 Water bridges: B:G.171 PSK.12: 9 residues within 4Å: Chain C: Y.46, T.98, S.169, G.170, L.173, I.207, A.238, L.241, H.289 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.173, C:I.207, C:L.241 Hydrogen bonds: C:G.170 Water bridges: C:Y.46, C:T.98, C:G.171 PSK.16: 7 residues within 4Å: Chain D: S.169, G.170, L.173, I.207, L.214, L.241, H.289 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.173, D:L.241 Hydrogen bonds: D:G.170 Water bridges: D:G.171

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

DMS.6: 2 residues within 4Å: Chain B: Q.213, E.216 No protein-ligand interaction detected (PLIP) DMS.7: 6 residues within 4Å: Chain B: P.200, H.203, R.248, H.275, 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.14: 2 residues within 4Å: Chain D: Q.213, E.216 No protein-ligand interaction detected (PLIP) DMS.15: 6 residues within 4Å: Chain D: P.200, H.203, R.248, H.275, 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

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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