SMTL ID : 6et9.1

Structure of the acetoacetyl-CoA-thiolase/HMG-CoA-synthase complex from Methanothermococcus thermolithotrophicus at 2.75 A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

hetero-4-4-4-mer

Ligands

3 x NA: SODIUM ION(Non-functional Binders)

NA.1: 7 residues within 4Å: Chain A: K.314, I.315, R.316, Y.319, F.322, V.323, T.324 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.315 NA.14: 5 residues within 4Å: Chain D: F.14, L.331, G.335, T.341, R.344 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.335, D:R.344 NA.34: 6 residues within 4Å: Chain J: W.27, P.148, G.149, D.150, E.153, Y.154 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:E.153, J:Y.154

11 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 1 residues within 4Å: Chain A: T.365 No protein-ligand interaction detected (PLIP) TRS.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) TRS.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) TRS.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) TRS.7: 2 residues within 4Å: Chain B: K.266 Chain D: D.45 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:D.45, B:K.266 TRS.9: 3 residues within 4Å: Chain A: K.266 Chain C: H.103, D.105 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.102, C:D.105 TRS.12: 1 residues within 4Å: Chain I: K.243 No protein-ligand interaction detected (PLIP) TRS.15: 3 residues within 4Å: Chain B: D.45, H.103 Chain D: K.266 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:K.266, D:K.266, B:H.103 TRS.22: 3 residues within 4Å: Chain F: W.6, K.10 Chain I: K.212 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain I Hydrogen bonds: F:W.6, F:K.10, I:K.212 TRS.24: 3 residues within 4Å: Chain G: W.6, K.10 Chain K: K.212 5 PLIP interactions: 3 interactions with chain G, 2 interactions with chain K Hydrogen bonds: G:W.6, G:K.10, G:K.10, K:K.212 Water bridges: K:K.212 TRS.27: 4 residues within 4Å: Chain A: E.19 Chain H: W.6, K.10 Chain J: K.212 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:K.212

8 x K: POTASSIUM ION(Non-covalent)

K.5: 5 residues within 4Å: Chain A: T.255, T.256, E.296, D.297, K.303 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.296 K.8: 4 residues within 4Å: Chain B: D.36, E.232, K.354, D.356 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.36 K.10: 3 residues within 4Å: Chain C: D.36, E.232, K.354 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.36 K.16: 3 residues within 4Å: Chain D: D.36, E.232, K.354 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.36, D:D.36 K.29: 2 residues within 4Å: Chain I: E.111 Chain K: E.111 2 PLIP interactions: 1 interactions with chain K, 1 interactions with chain I Metal complexes: K:E.111, I:E.111 K.30: 2 residues within 4Å: Chain I: D.3, G.129 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:D.3 K.35: 2 residues within 4Å: Chain J: E.111 Chain L: E.111 2 PLIP interactions: 1 interactions with chain J, 1 interactions with chain L Metal complexes: J:E.111, L:E.111 K.37: 3 residues within 4Å: Chain K: E.72, A.101, D.104 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:E.72, K:A.101

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

CL.11: 3 residues within 4Å: Chain C: G.41 Chain F: R.38, R.39 Ligand excluded by PLIP CL.19: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain B: G.41 Chain E: R.38, R.39 Ligand excluded by PLIP CL.25: 3 residues within 4Å: Chain D: G.41 Chain G: R.38, R.39 Ligand excluded by PLIP CL.28: 2 residues within 4Å: Chain H: R.38, R.39 Ligand excluded by PLIP CL.31: 6 residues within 4Å: Chain I: V.88, K.89, P.90 Chain K: E.111, F.112, A.113 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-covalent)

MG.13: 1 residues within 4Å: Chain D: N.38 No protein-ligand interaction detected (PLIP)

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.32: 1 residues within 4Å: Chain I: M.225 No protein-ligand interaction detected (PLIP) GOL.33: 1 residues within 4Å: Chain I: E.32 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:E.32 GOL.36: 1 residues within 4Å: Chain J: Y.267 No protein-ligand interaction detected (PLIP) GOL.38: 1 residues within 4Å: Chain K: N.177 1 PLIP interactions: 1 interactions with chain K Water bridges: K:K.224 GOL.39: 2 residues within 4Å: Chain L: K.19, Y.334 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:K.19, L:Y.334

4 x ZN: ZINC ION(Non-covalent)

ZN.18: 4 residues within 4Å: Chain E: C.20, C.23, C.34, C.37 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.20, E:C.23, E:C.34, E:C.37 ZN.21: 4 residues within 4Å: Chain F: C.20, C.23, C.34, C.37 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.20, F:C.23, F:C.34, F:C.37 ZN.23: 4 residues within 4Å: Chain G: C.20, C.23, C.34, C.37 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.20, G:C.23, G:C.34, G:C.37 ZN.26: 4 residues within 4Å: Chain H: C.20, C.23, C.34, C.37 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.20, H:C.23, H:C.34, H:C.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vogeli, B. et al., Archaeal acetoacetyl-CoA thiolase/HMG-CoA synthase complex channels the intermediate via a fused CoA-binding site. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-03-14

Peptides

Acetyl-CoA acetyltransferase thiolase: ABCD
Pfam DUF35: EFGH
HydroxyMethylGlutaryl-CoA synthase: IJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

Acetyl-CoA acetyltransferase thiolase

Pfam DUF35

HydroxyMethylGlutaryl-CoA synthase

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