SMTL ID : 5m45.1 (1 other biounit)

Structure of Acetone Carboxylase purified from Xanthobacter autotrophicus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: H.150, D.153, H.175 Ligands: ACT.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.150, A:D.153, A:D.153, A:H.175, ACT.2 MN.14: 4 residues within 4Å: Chain D: H.150, D.153, H.175 Ligands: ACT.15 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:H.150, D:D.153, D:D.153, D:H.175, ACT.15

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 8 residues within 4Å: Chain A: H.150, D.153, H.175, M.187, W.401, F.456, W.479 Ligands: MN.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.401, A:F.456, A:W.479 Salt bridges: A:H.150, A:H.175 ACT.3: 4 residues within 4Å: Chain A: E.53, P.54, I.55, L.56 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.55, A:L.56 ACT.11: 7 residues within 4Å: Chain A: V.69, E.73 Chain B: R.123, K.328, G.458, K.459 Ligands: MG.10 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:K.459, A:V.69 Water bridges: B:R.123 Salt bridges: B:R.123, B:K.328, B:K.459 ACT.15: 8 residues within 4Å: Chain D: H.150, D.153, H.175, M.187, W.401, F.456, W.479 Ligands: MN.14 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:W.401, D:F.456, D:W.479 Salt bridges: D:H.150, D:H.175 ACT.16: 4 residues within 4Å: Chain D: E.53, P.54, I.55, L.56 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:I.55, D:L.56 ACT.24: 6 residues within 4Å: Chain D: V.69, E.73 Chain E: R.123, G.458, K.459 Ligands: MG.23 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain D Water bridges: E:R.123 Salt bridges: E:R.123, E:K.459 Hydrophobic interactions: D:V.69

2 x AE4: 3,6,9,12,15-PENTAOXAHEPTADECAN-1-OL(Non-covalent)

AE4.4: 8 residues within 4Å: Chain A: K.36, G.113, G.116, A.117, K.120, A.375, Y.376, F.773 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.113 Water bridges: A:R.28, A:G.116, A:Y.376, A:Y.376 AE4.17: 9 residues within 4Å: Chain D: M.32, G.113, G.116, A.117, K.120, A.375, Y.376, Q.772, F.773 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.113 Water bridges: D:R.28, D:R.28, D:G.116, D:K.120

12 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.5: 2 residues within 4Å: Chain A: S.763, V.768 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.763, A:V.768, H2O.12 MG.6: 1 residues within 4Å: Chain A: S.759 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.759, A:S.759, H2O.8, H2O.13, H2O.18 MG.8: 3 residues within 4Å: Chain B: M.22, D.24 Ligands: AMP.7 5 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: B:M.22, AMP.7, H2O.27, H2O.29, H2O.31 MG.9: 2 residues within 4Å: Chain B: D.309 Ligands: AMP.7 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.309, B:D.309, H2O.23, H2O.25, H2O.33 MG.10: 1 residues within 4Å: Ligands: ACT.11 4 PLIP interactions: 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: ACT.11, H2O.31, H2O.33, H2O.36 MG.12: 2 residues within 4Å: Chain B: D.447 Chain C: D.19 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.19, H2O.29, H2O.32, H2O.42, H2O.42 MG.18: 2 residues within 4Å: Chain D: S.763, V.768 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:S.763, D:V.768, H2O.51, H2O.60, H2O.62 MG.19: 1 residues within 4Å: Chain D: A.689 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:A.689, H2O.51, H2O.89 MG.21: 2 residues within 4Å: Chain E: D.309 Ligands: AMP.20 5 PLIP interactions: 2 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.309, E:D.309, H2O.66, H2O.66, H2O.78 MG.22: 3 residues within 4Å: Chain E: M.22, D.24 Ligands: AMP.20 5 PLIP interactions: 1 interactions with chain E, 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: E:M.22, AMP.20, H2O.70, H2O.71, H2O.74 MG.23: 1 residues within 4Å: Ligands: ACT.24 3 PLIP interactions: 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: ACT.24, H2O.75, H2O.81 MG.25: 2 residues within 4Å: Chain E: D.447 Chain F: D.19 5 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: E:D.447, F:D.19, H2O.79, H2O.86, H2O.87

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.7: 19 residues within 4Å: Chain B: G.20, T.21, M.22, G.311, G.312, A.352, L.400, N.404, F.405, L.406, G.473, A.474, S.691, D.692, A.693, T.694, T.695 Ligands: MG.8, MG.9 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:T.21, B:T.21, B:M.22, B:G.312, B:N.404, B:L.406, B:G.473 Water bridges: B:D.17, B:D.17, B:G.20, B:T.21, B:G.312, B:S.391, B:N.404 AMP.20: 19 residues within 4Å: Chain E: G.20, T.21, M.22, G.311, G.312, A.352, L.400, N.404, F.405, L.406, G.473, A.474, S.691, D.692, A.693, T.694, T.695 Ligands: MG.21, MG.22 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:T.21, E:T.21, E:T.21, E:M.22, E:G.312, E:N.404, E:L.406, E:G.473 Water bridges: E:D.17, E:G.20, E:M.22, E:S.391

2 x ZN: ZINC ION(Non-covalent)

ZN.13: 4 residues within 4Å: Chain C: C.74, C.76, C.124, C.127 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.74, C:C.76, C:C.124, C:C.127 ZN.26: 4 residues within 4Å: Chain F: C.74, C.76, C.124, C.127 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.74, F:C.76, F:C.124, F:C.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mus, F. et al., Structural Basis for the Mechanism of ATP-Dependent Acetone Carboxylation. Sci Rep (2017)

Release Date

2017-08-09

Peptides

Acetone carboxylase alpha subunit: AD
Acetone carboxylase beta subunit: BE
Acetone carboxylase gamma subunit: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

Acetone carboxylase alpha subunit

Acetone carboxylase beta subunit

Acetone carboxylase gamma subunit

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