SMTL ID : 6eej.1

Streptomyces bingchenggensis Aldolase-Dehydratase in covalent complex with dienone product.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-tetramer

Ligands

4 x J6S: (3E,5E)-6-(4-nitrophenyl)-2-oxohexa-3,5-dienoic acid(Covalent)

J6S.1: 18 residues within 4Å: Chain A: Y.24, M.61, I.63, W.65, Y.82, E.84, L.86, I.104, A.111, R.114, G.115, Q.118, F.120, K.122, M.178, V.182, L.209, F.252 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.86, A:F.120, A:F.120, A:K.122, A:L.209, A:F.252 Hydrogen bonds: A:Y.24, A:A.111, A:Q.118 Salt bridges: A:R.114, A:K.122 J6S.4: 16 residues within 4Å: Chain B: Y.24, M.61, I.63, W.65, Y.82, E.84, L.86, A.111, R.114, G.115, Q.118, F.120, K.122, V.182, L.209, F.252 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.86, B:F.120, B:F.120, B:K.122, B:F.252 Hydrogen bonds: B:Y.24, B:A.111, B:Q.118 Salt bridges: B:R.114, B:K.122 J6S.7: 18 residues within 4Å: Chain C: Y.24, M.61, I.63, W.65, Y.82, E.84, L.86, I.104, A.111, R.114, G.115, Q.118, F.120, K.122, M.178, V.182, L.209, F.252 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:W.65, C:L.86, C:F.120, C:F.120, C:K.122, C:F.252 Hydrogen bonds: C:Y.24, C:Q.118 Salt bridges: C:R.114, C:K.122 J6S.10: 18 residues within 4Å: Chain D: Y.24, M.61, I.63, W.65, Y.82, E.84, L.86, I.104, A.111, R.114, G.115, Q.118, F.120, K.122, M.178, V.182, L.209, F.252 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:F.120, D:F.120, D:K.122, D:F.252 Hydrogen bonds: D:Y.24, D:Q.118 Water bridges: D:S.207 Salt bridges: D:R.114, D:K.122

5 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 6 residues within 4Å: Chain A: K.164, I.165, T.166, T.221, A.222, D.223 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.164, A:T.221 Water bridges: A:A.222 FMT.5: 6 residues within 4Å: Chain B: K.164, I.165, T.166, T.221, A.222, D.223 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.164, B:T.221, B:T.221 Water bridges: B:A.222 FMT.8: 6 residues within 4Å: Chain C: K.164, I.165, T.166, T.221, A.222, D.223 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.164, C:T.166 Water bridges: C:A.222 FMT.11: 6 residues within 4Å: Chain D: K.164, I.165, T.166, T.221, A.222, D.223 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.164, D:T.166, D:T.221 Water bridges: D:A.222, D:D.223 FMT.12: 4 residues within 4Å: Chain D: A.132, Y.133, S.134, L.143 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.134 Water bridges: D:S.134

4 x K: POTASSIUM ION(Non-covalent)

K.3: 5 residues within 4Å: Chain A: G.137, P.138, T.140, P.141, V.142 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.137, A:T.140, H2O.8, H2O.9 K.6: 5 residues within 4Å: Chain B: G.137, P.138, T.140, P.141, V.142 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:G.137, B:T.140, H2O.18, H2O.19 K.9: 5 residues within 4Å: Chain C: G.137, P.138, T.140, P.141, V.142 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:G.137, C:T.140, H2O.28, H2O.30 K.13: 5 residues within 4Å: Chain D: G.137, P.138, T.140, P.141, V.142 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:G.137, D:T.140, H2O.38, H2O.39, H2O.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mydy, L.S. et al., Mechanistic Studies of theStreptomyces bingchenggensisAldolase-Dehydratase: Implications for Substrate and Reaction Specificity in the Acetoacetate Decarboxylase-like Superfamily. Biochemistry (2019)

Release Date

2019-08-14

Peptides

Acetoacetate decarboxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Acetoacetate decarboxylase