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

Pikromycin thioesterase with covalent pentaketide affinity label

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 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 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.62 Salt bridges: A:R.236, B:R.45 SO4.2: 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 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.62, B:Q.62 Salt bridges: B:R.236, A:R.45 SO4.8: 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 SO4.9: 1 residues within 4Å: Chain C: R.269 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.269 SO4.12: 4 residues within 4Å: Chain C: R.45 Chain D: A.58, Q.62, R.236 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Salt bridges: C:R.45, D:R.236 Hydrogen bonds: D:Q.62, D:Q.62

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: H.275, D.277, L.278 Chain C: H.275, D.277 Ligands: MG.10 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.277, H2O.2 MG.10: 6 residues within 4Å: Chain A: H.275, D.277 Chain C: H.275, D.277, L.278 Ligands: MG.3 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.277, H2O.18

2 x YML: [(3R,4S,5S,7R)-4,8-DIHYDROXY-3,5,7-TRIMETHYL-2-OXOOCTYL]PHOSPHONIC ACID(Covalent)

YML.4: 11 residues within 4Å: Chain A: Y.46, L.50, T.98, A.99, S.169, G.170, Q.204, I.207, M.234, L.241, H.289 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.50, A:T.98, A:I.207, A:L.241 Hydrogen bonds: A:T.98, A:G.170 Water bridges: A:T.98, A:G.171, A:Q.204, A:Q.204 YML.11: 11 residues within 4Å: Chain C: Y.46, L.50, T.98, A.99, S.169, G.170, Q.204, I.207, M.234, L.241, H.289 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:L.50, C:T.98, C:I.207, C:L.241 Hydrogen bonds: C:T.98, C:G.170 Water bridges: C:T.98, C:G.171, C:Q.204, C:Q.204

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

DMS.6: 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.7: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.216 DMS.13: 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 DMS.14: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain D Water bridges: D:E.216

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Akey, D.L. et al., Structural Basis for Macrolactonization by the Pikromycin Thioesterase. 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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