SMTL ID : 4zbt.1

Streptomyces bingchenggensis aldolase-dehydratase in Schiff base complex with pyruvate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x PYR: PYRUVIC ACID(Covalent)

PYR.1: 10 residues within 4Å: Chain A: Y.24, Y.82, E.84, I.104, A.111, R.114, G.115, Q.118, F.120, K.122 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.120, A:K.122 Hydrogen bonds: A:Y.24, A:Q.118, A:Q.118 Salt bridges: A:R.114, A:K.122 PYR.4: 10 residues within 4Å: Chain B: Y.24, Y.82, E.84, I.104, A.111, R.114, G.115, Q.118, F.120, K.122 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.120, B:K.122 Hydrogen bonds: B:Y.24, B:Q.118, B:Q.118 Salt bridges: B:R.114, B:K.122 PYR.6: 10 residues within 4Å: Chain C: Y.24, Y.82, E.84, I.104, A.111, R.114, G.115, Q.118, F.120, K.122 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.120, C:K.122 Hydrogen bonds: C:Y.24, C:A.111, C:Q.118 Salt bridges: C:R.114, C:K.122 PYR.11: 10 residues within 4Å: Chain D: Y.24, Y.82, E.84, I.104, A.111, R.114, G.115, Q.118, F.120, K.122 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:F.120, D:K.122 Hydrogen bonds: D:Y.24, D:A.111, D:Q.118 Salt bridges: D:R.114, D:K.122

6 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.164, A:T.166, A:T.221, A:A.222 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 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.164, B:T.166, B:T.221 Water bridges: B:A.222, B:D.223 FMT.7: 4 residues within 4Å: Chain C: A.193, G.194, Q.195, H.196 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.194, C:H.196 Water bridges: C:H.196 FMT.8: 6 residues within 4Å: Chain C: K.164, I.165, T.166, T.221, A.222, D.223 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.164, C:T.166, C:T.166, C:T.221 Water bridges: C:A.222 FMT.12: 10 residues within 4Å: Chain A: H.23, Y.24, A.25, A.251, Y.252 Chain D: G.136, G.137, P.138, G.139, T.140 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:Y.24, A:Y.252, A:Y.252, D:G.139 FMT.13: 4 residues within 4Å: Chain D: A.193, G.194, Q.195, H.196 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.194, D:H.196 Water bridges: D:H.196

2 x PE4: 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-functional Binders)

PE4.3: 11 residues within 4Å: Chain A: G.71, L.72, E.73, L.75, D.76 Chain C: H.230 Chain D: T.152, R.159, E.162, A.163, K.164 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:K.164 PE4.10: 11 residues within 4Å: Chain A: H.230 Chain B: G.150, A.151, T.152, E.162, A.163 Chain C: G.71, L.72, E.73, L.75, D.76 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: C:E.73 Hydrophobic interactions: B:T.152 Water bridges: A:H.230

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.9: 10 residues within 4Å: Chain B: L.75, D.76 Chain C: G.150, A.151, T.152, R.159, E.162, A.163, K.164 Chain D: H.230 No protein-ligand interaction detected (PLIP) PEG.14: 9 residues within 4Å: Chain A: G.150, A.151, T.152, E.162, A.163, K.164 Chain B: H.230 Chain D: L.75, D.76 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.163

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mydy, L.S. et al., Sbi00515, a Protein of Unknown Function from Streptomyces bingchenggensis, Highlights the Functional Versatility of the Acetoacetate Decarboxylase Scaffold. Biochemistry (2015)

Release Date

2015-06-17

Peptides

Acetoacetate decarboxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Acetoacetate decarboxylase

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