SMTL ID : 4zbo.1

Streptomyces bingchenggensis acetoacetate decarboxylase in non-covalent complex with potassium formate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-tetramer

Ligands

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

FMT.1: 7 residues within 4Å: Chain A: Y.24, Y.82, A.111, R.114, G.115, Q.118, K.122 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.24, A:R.114, A:R.114, A:Q.118, A:K.122 Water bridges: A:Y.82, A:Y.82, A:E.84 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:K.164, A:T.166, A:T.221 Water bridges: A:A.222 FMT.3: 6 residues within 4Å: Chain A: G.137, P.138, T.140, P.141, V.142 Chain D: Y.74 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:G.137, D:Y.74, D:Y.74 Water bridges: A:V.142 FMT.6: 7 residues within 4Å: Chain B: Y.24, Y.82, A.111, R.114, G.115, Q.118, K.122 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Y.24, B:R.114, B:R.114, B:Q.118, B:K.122 Water bridges: B:Y.82, B:Y.82, B:E.84, B:E.84 FMT.7: 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.10: 7 residues within 4Å: Chain C: Y.24, Y.82, A.111, R.114, G.115, Q.118, K.122 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Y.24, C:R.114, C:R.114, C:Q.118, C:K.122 Water bridges: C:E.84, C:E.84 FMT.11: 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:K.164, C:T.166, C:T.221 Water bridges: C:A.222 FMT.12: 4 residues within 4Å: Chain B: R.131 Chain C: A.132, Y.133, S.134 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain C Water bridges: B:R.131, B:R.131, C:A.132 Hydrogen bonds: C:S.134, C:S.134, C:S.134 FMT.15: 6 residues within 4Å: Chain A: Y.74 Chain D: G.137, P.138, T.140, P.141, V.142 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:G.137 Water bridges: D:P.138, A:Y.74 FMT.16: 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, D:D.223 Water bridges: D:A.222 FMT.17: 7 residues within 4Å: Chain D: Y.24, Y.82, A.111, R.114, G.115, Q.118, K.122 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Y.24, D:R.114, D:R.114, D:Q.118, D:K.122 Water bridges: D:E.84

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

PEG.4: 4 residues within 4Å: Chain A: P.228, A.229, H.230 Chain B: L.227 No protein-ligand interaction detected (PLIP) PEG.9: 4 residues within 4Å: Chain A: L.227 Chain B: P.228, A.229, H.230 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.230 PEG.13: 7 residues within 4Å: Chain B: L.75, D.76 Chain C: T.152, E.162, A.163, K.164 Chain D: H.230 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.163 Water bridges: C:E.162 PEG.14: 4 residues within 4Å: Chain C: P.228, A.229, H.230 Chain D: L.227 No protein-ligand interaction detected (PLIP) PEG.18: 8 residues within 4Å: Chain A: G.150, 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

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

PE4.5: 15 residues within 4Å: Chain A: T.70, G.71, L.72, E.73, L.75, D.76 Chain C: H.230 Chain D: G.150, A.151, T.152, R.159, E.162, A.163, K.164, D.223 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A, 1 interactions with chain C Water bridges: D:R.159, A:D.76, C:H.230

1 x ETE: 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-covalent)

ETE.8: 12 residues within 4Å: Chain A: H.230 Chain B: G.150, T.152, R.159, E.162, A.163, K.164, D.223, L.224, A.225 Chain C: L.75, D.76 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.230

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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