SMTL ID : 8vzj.1 (1 other biounit)

Crystal Structure of 2-Hydroxyacyl-CoA Lyase/Synthase DhcHACS from Dehalococcoidia bacterium in the Complex with THDP and ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

4 x TPP: THIAMINE DIPHOSPHATE

TPP.1: 25 residues within 4Å: Chain A: Y.370, G.391, A.392, S.393, T.394, G.417, M.419, G.443, D.444, S.445, A.446, F.449, N.472, G.474, I.475, G.476 Chain B: I.28, V.29, E.53, V.76, P.79, G.80, H.83, Q.116 Ligands: MG.4 15 PLIP interactions: 4 interactions with chain B, 11 interactions with chain A Hydrophobic interactions: B:I.28, B:V.76, B:P.79, A:I.475 Hydrogen bonds: B:Q.116, A:A.392, A:S.393, A:T.394, A:G.417, A:M.419, A:S.445, A:S.445, A:A.446, A:N.472, A:G.476 TPP.5: 26 residues within 4Å: Chain A: I.28, V.29, E.53, V.76, P.79, G.80, H.83, Q.116 Chain B: Y.370, G.391, A.392, S.393, T.394, G.417, M.419, G.443, D.444, S.445, A.446, F.449, N.472, G.474, I.475, G.476, G.477 Ligands: MG.8 17 PLIP interactions: 13 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.475, A:I.28, A:V.76, A:P.79 Hydrogen bonds: B:Y.370, B:A.392, B:S.393, B:T.394, B:G.417, B:M.419, B:S.445, B:S.445, B:A.446, B:N.472, B:G.476, B:G.477, A:Q.116 TPP.9: 26 residues within 4Å: Chain C: Y.370, G.391, A.392, S.393, T.394, G.417, T.418, M.419, G.443, D.444, S.445, A.446, F.449, N.472, G.474, I.475, G.476 Chain D: I.28, V.29, E.53, V.76, P.79, G.80, H.83, Q.116 Ligands: MG.11 17 PLIP interactions: 13 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:I.475, C:I.475, D:I.28, D:V.76, D:P.79 Hydrogen bonds: C:A.392, C:S.393, C:T.394, C:G.417, C:M.419, C:S.445, C:A.446, C:N.472, C:G.476, D:Q.116 Water bridges: C:D.444, C:N.472 TPP.12: 25 residues within 4Å: Chain C: I.28, V.29, E.53, V.76, P.79, G.80, H.83, Q.116 Chain D: Y.370, G.391, A.392, S.393, T.394, G.417, M.419, G.443, D.444, S.445, A.446, F.449, N.472, G.474, I.475, G.476 Ligands: MG.15 22 PLIP interactions: 18 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:M.419, D:F.449, D:I.475, D:I.475, C:I.28, C:V.76, C:P.79 Hydrogen bonds: D:Y.370, D:A.392, D:S.393, D:T.394, D:T.394, D:T.394, D:G.417, D:M.419, D:D.444, D:S.445, D:S.445, D:A.446, D:N.472, D:G.476, C:Q.116

4 x ADP: ADENOSINE-5'-DIPHOSPHATE

ADP.2: 20 residues within 4Å: Chain A: C.95, R.155, G.214, K.215, G.216, Y.219, S.220, S.240, G.273, A.274, R.275, N.277, M.279, D.298, I.299, S.300, G.316, D.317, A.318, S.415 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:R.155, A:R.155, A:K.215, A:S.220, A:S.240, A:S.240, A:R.275, A:R.275, A:N.277, A:I.299, A:S.300, A:D.317, A:A.318, A:S.415, A:S.415 Salt bridges: A:K.215, A:K.215, A:R.275 ADP.6: 21 residues within 4Å: Chain B: C.95, R.155, P.156, G.214, K.215, G.216, Y.219, S.220, S.240, G.273, A.274, R.275, N.277, M.279, D.298, I.299, S.300, G.316, D.317, A.318, S.415 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:R.155, B:R.155, B:K.215, B:S.240, B:S.240, B:R.275, B:R.275, B:R.275, B:N.277, B:I.299, B:D.317, B:D.317, B:A.318, B:S.415, B:S.415 Salt bridges: B:K.215, B:K.215, B:R.275 ADP.10: 21 residues within 4Å: Chain C: C.95, R.155, G.214, K.215, G.216, Y.219, S.220, S.240, G.273, A.274, R.275, N.277, M.279, D.298, I.299, S.300, E.303, G.316, D.317, A.318, S.415 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:R.155, C:R.155, C:K.215, C:S.220, C:S.240, C:R.275, C:R.275, C:N.277, C:I.299, C:S.300, C:D.317, C:D.317, C:A.318, C:S.415, C:S.415 Salt bridges: C:K.215, C:K.215, C:R.275 ADP.13: 20 residues within 4Å: Chain D: C.95, R.155, G.214, K.215, G.216, Y.219, S.220, S.240, G.273, A.274, R.275, N.277, M.279, M.280, D.298, I.299, S.300, G.316, D.317, A.318 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:R.155, D:R.155, D:K.215, D:S.240, D:S.240, D:R.275, D:R.275, D:N.277, D:I.299, D:S.300, D:D.317, D:A.318 Salt bridges: D:K.215, D:K.215, D:R.275

2 x GOL: GLYCEROL

GOL.3: 4 residues within 4Å: Chain A: W.92, S.93, C.95, R.275 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.275, A:R.275 GOL.7: 5 residues within 4Å: Chain B: W.92, S.93, C.95, R.155, R.275 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.92, B:R.155, B:R.275

4 x MG: MAGNESIUM ION

MG.4: 5 residues within 4Å: Chain A: D.444, N.472, G.474, G.476 Ligands: TPP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.444, A:G.474 MG.8: 4 residues within 4Å: Chain B: D.444, N.472, G.474 Ligands: TPP.5 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.444, B:G.474 MG.11: 5 residues within 4Å: Chain C: D.444, N.472, G.474, G.476 Ligands: TPP.9 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.444, C:G.474, H2O.1 MG.15: 6 residues within 4Å: Chain D: D.444, N.472, G.474, G.476, G.477 Ligands: TPP.12 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.444, D:G.474, H2O.1

1 x EDO: 1,2-ETHANEDIOL

EDO.14: 3 residues within 4Å: Chain D: W.92, S.93, R.155 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.93, D:R.155

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Revealing reaction intermediates in one-carbon elongation by thiamine diphosphate/CoA-dependent enzyme family. Commun Chem (2024)

Release Date

2024-10-02

Peptides

Oxalyl-CoA decarboxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

D
F

Oxalyl-CoA decarboxylase

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