SMTL ID : 4k4d.1

X-ray crystal structure of E. coli YbdB complexed with 2,4-dihydroxyphenacyl-CoA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

homo-dimer

Ligands

2 x HFQ: 2,4-dihydroxyphenacyl coenzyme A(Non-covalent)

HFQ.1: 18 residues within 4Å: Chain A: Q.48, P.49, L.53, H.54, G.55, H.89, H.90, R.91, P.92 Chain B: E.63, T.64, S.67, M.68, V.81, G.82, T.83, L.136 Ligands: ACT.5 11 PLIP interactions: 6 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:Q.48, A:H.89, B:V.81, B:V.81, B:T.83, B:L.136 Hydrogen bonds: A:H.54, A:G.55, A:H.89, A:H.90, B:G.82 HFQ.3: 18 residues within 4Å: Chain A: E.63, T.64, S.67, M.68, V.81, G.82, A.134, L.136 Chain B: Q.48, P.49, L.53, H.54, G.55, H.89, H.90, R.91, P.92 Ligands: ACT.4 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Q.48, B:H.89, A:V.81, A:A.134, A:L.136 Hydrogen bonds: B:G.55, B:H.89, B:H.90, A:G.82 Salt bridges: B:R.91

1 x MLI: MALONATE ION(Non-functional Binders)

MLI.2: 2 residues within 4Å: Chain A: L.9, D.10 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.10, A:D.10

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

ACT.4: 5 residues within 4Å: Chain A: M.68, F.71 Chain B: P.49, F.50 Ligands: HFQ.3 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.49, A:F.71 ACT.5: 5 residues within 4Å: Chain A: P.49 Chain B: T.15, M.68, F.71 Ligands: HFQ.1 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.71 Hydrogen bonds: B:T.15

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, R. et al., Structure and Catalysis in the Escherichia coli Hotdog-fold Thioesterase Paralogs YdiI and YbdB. Biochemistry (2014)

Release Date

2014-07-30

Peptides

Proofreading thioesterase EntH: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Proofreading thioesterase EntH

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