SMTL ID : 4k4b.3 (3 other biounits)

X-ray crystal structure of E. coli YdiI complexed with undeca-2-one-CoA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

4 x UOQ: undeca-2-one coenzyme A(Non-covalent)

UOQ.1: 13 residues within 4Å: Chain A: V.42, D.43, S.44, K.47, Q.48, P.49, E.95, G.96 Chain B: A.11, M.15, E.17, G.18, N.19 11 PLIP interactions: 2 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:A.11 Hydrogen bonds: B:N.19, A:S.44, A:G.96 Water bridges: A:V.42, A:D.43, A:K.47, A:K.47, A:K.47 Salt bridges: A:K.47, A:K.47 UOQ.3: 5 residues within 4Å: Chain A: H.106, G.108, S.109, R.110, H.111 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.109, A:S.109, A:R.110, A:H.111, A:H.111 Salt bridges: A:H.106, A:H.106, A:H.111 UOQ.4: 20 residues within 4Å: Chain A: Q.48, P.49, L.53, H.54, G.55, H.89, V.90, R.91, S.92 Chain B: L.12, M.15, V.21, F.28, E.63, S.67, V.68, V.81, G.82, L.83, L.136 14 PLIP interactions: 7 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:Q.48, A:P.49, B:M.15, B:V.21, B:F.28, B:V.68, B:V.81, B:L.83 Hydrogen bonds: A:Q.48, A:G.55, A:H.89, A:V.90, A:S.92, B:G.82 UOQ.5: 5 residues within 4Å: Chain B: H.106, G.108, S.109, R.110, H.111 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.109, B:R.110, B:R.110, B:H.111 Salt bridges: B:H.106, B:R.110, B:R.110, B:H.111

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

CL.2: 3 residues within 4Å: Chain A: Y.71, K.79, V.80 Ligand excluded by PLIP

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

Esterase YdiI: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

Esterase YdiI

Related Entries With Identical Sequence