SMTL ID : 8vzh.1

Crystal Structure of 2-Hydroxyacyl-CoA lyase/synthase TbHACS from Thermoflexaceae bacterium in the Complex with THDP and ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-tetramer

Ligands

4 x ADP: ADENOSINE-5'-DIPHOSPHATE

ADP.1: 21 residues within 4Å: Chain A: N.92, R.152, G.211, K.212, G.213, Y.216, S.217, S.237, G.270, A.271, R.272, N.274, M.276, D.295, I.296, S.297, G.313, D.314, A.315, T.412 Ligands: EDO.4 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:R.152, A:R.152, A:K.212, A:S.217, A:S.237, A:S.237, A:R.272, A:R.272, A:N.274, A:I.296, A:D.314, A:D.314, A:A.315, A:T.412 Water bridges: A:S.237, A:G.240, A:R.272, A:T.412 Salt bridges: A:K.212, A:K.212, A:R.272 ADP.11: 20 residues within 4Å: Chain B: R.152, G.211, K.212, G.213, Y.216, S.217, S.237, G.270, A.271, R.272, N.274, M.276, D.295, I.296, S.297, G.313, D.314, A.315, T.412 Ligands: EDO.13 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:R.152, B:R.152, B:K.212, B:S.237, B:S.237, B:R.272, B:R.272, B:N.274, B:I.296, B:D.314, B:A.315 Water bridges: B:S.237, B:N.274, B:T.412, B:T.412 Salt bridges: B:K.212, B:K.212, B:R.272 ADP.19: 20 residues within 4Å: Chain C: R.152, G.211, K.212, G.213, Y.216, S.217, S.237, G.270, A.271, R.272, N.274, M.276, D.295, I.296, S.297, G.313, D.314, A.315, T.412 Ligands: EDO.21 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:R.152, C:R.152, C:K.212, C:S.217, C:S.237, C:S.237, C:R.272, C:R.272, C:N.274, C:I.296, C:D.314, C:D.314, C:A.315, C:T.412 Water bridges: C:S.237, C:R.272, C:T.412 Salt bridges: C:K.212, C:K.212, C:R.272 ADP.28: 21 residues within 4Å: Chain D: N.92, R.152, G.211, K.212, G.213, Y.216, S.217, S.237, G.270, A.271, R.272, N.274, M.276, D.295, I.296, S.297, G.313, D.314, A.315, T.412 Ligands: EDO.30 21 PLIP interactions: 21 interactions with chain D Hydrogen bonds: D:R.152, D:R.152, D:K.212, D:S.217, D:S.237, D:S.237, D:R.272, D:R.272, D:N.274, D:I.296, D:D.314, D:A.315 Water bridges: D:K.212, D:S.237, D:G.240, D:N.274, D:T.412, D:T.412 Salt bridges: D:K.212, D:K.212, D:R.272

4 x TPP: THIAMINE DIPHOSPHATE

TPP.2: 25 residues within 4Å: Chain A: Y.367, G.388, A.389, S.390, T.391, G.414, M.416, G.440, D.441, S.442, A.443, F.446, N.468, G.470, I.471, G.472 Chain B: I.25, V.26, E.50, V.73, P.76, G.77, H.80, Q.113 Ligands: MG.9 20 PLIP interactions: 15 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:I.471, A:I.471, B:I.25, B:V.73, B:P.76 Hydrogen bonds: A:A.389, A:S.390, A:T.391, A:T.391, A:G.414, A:M.416, A:S.442, A:A.443, A:G.472, A:G.473, B:Q.113 Water bridges: A:D.441, A:N.468, A:N.468, B:V.73 TPP.12: 26 residues within 4Å: Chain A: I.25, V.26, E.50, V.73, P.76, G.77, H.80, Q.113 Chain B: Y.367, G.388, A.389, S.390, T.391, G.414, M.416, G.440, D.441, S.442, A.443, F.446, N.468, G.470, I.471, G.472, G.473 Ligands: MG.17 21 PLIP interactions: 17 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.471, B:I.471, A:I.25, A:V.73 Hydrogen bonds: B:Y.367, B:A.389, B:S.390, B:T.391, B:G.414, B:M.416, B:S.442, B:A.443, B:N.468, B:N.468, B:G.472, B:G.473, A:Q.113 Water bridges: B:S.390, B:D.441, B:D.441, A:E.50 TPP.20: 27 residues within 4Å: Chain C: Y.367, G.388, A.389, S.390, T.391, G.414, M.416, G.440, D.441, S.442, A.443, F.446, N.468, G.470, I.471, G.472, G.473 Chain D: I.25, V.26, E.50, V.73, P.76, G.77, H.80, Q.113 Ligands: EDO.23, MG.25 21 PLIP interactions: 16 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:I.471, D:I.25, D:V.73, D:P.76 Hydrogen bonds: C:Y.367, C:A.389, C:S.390, C:T.391, C:G.414, C:M.416, C:S.442, C:A.443, C:N.468, C:N.468, C:G.472, C:G.473, D:Q.113 Water bridges: C:S.390, C:T.391, C:D.441, D:V.73 TPP.29: 25 residues within 4Å: Chain C: I.25, V.26, E.50, V.73, P.76, G.77, H.80, Q.113 Chain D: Y.367, G.388, A.389, S.390, T.391, G.414, M.416, G.440, D.441, S.442, A.443, F.446, N.468, G.470, I.471, G.472 Ligands: MG.33 20 PLIP interactions: 15 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:I.471, D:I.471, C:I.25, C:V.73, C:P.76 Hydrogen bonds: D:A.389, D:S.390, D:T.391, D:T.391, D:G.414, D:M.416, D:D.441, D:S.442, D:A.443, D:N.468, D:G.472, C:Q.113 Water bridges: D:D.441, D:N.468, C:V.73

11 x EDO: 1,2-ETHANEDIOL

EDO.3: 10 residues within 4Å: Chain A: E.387, G.417, V.418, G.419, A.420, Q.439, A.443, F.444, G.447, G.448 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.417, A:A.420, A:G.421, A:Q.439, A:F.444 Water bridges: A:G.419 EDO.4: 9 residues within 4Å: Chain A: Y.62, N.91, N.92, W.93, P.153, K.212, G.213, Y.216 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.92 EDO.6: 6 residues within 4Å: Chain A: G.302, N.304, V.305, P.306 Chain C: F.139, P.177 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Water bridges: C:E.142, A:N.304 EDO.7: 5 residues within 4Å: Chain A: S.104, N.107, R.130 Chain D: R.130, D.132 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:R.130 Water bridges: A:S.104, D:R.130, D:R.130, D:D.132 EDO.13: 8 residues within 4Å: Chain B: Y.62, N.91, N.92, W.93, K.212, G.213, Y.216 Ligands: ADP.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.92, B:K.212 EDO.14: 7 residues within 4Å: Chain B: G.302, N.304, V.305, P.306 Chain D: F.139, E.142, P.177 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Water bridges: B:G.302, D:E.142 EDO.21: 8 residues within 4Å: Chain C: Y.62, N.91, N.92, W.93, P.153, K.212, Y.216 Ligands: ADP.19 No protein-ligand interaction detected (PLIP) EDO.22: 3 residues within 4Å: Chain C: T.341, G.342, S.345 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.341 EDO.23: 7 residues within 4Å: Chain C: G.388, A.389, M.392, G.414, M.416 Chain D: F.112 Ligands: TPP.20 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.414 EDO.30: 9 residues within 4Å: Chain D: Y.62, N.91, N.92, W.93, P.153, K.212, G.213, Y.216 Ligands: ADP.28 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.92, D:K.212 EDO.31: 7 residues within 4Å: Chain B: F.139, E.142, P.177 Chain D: G.302, N.304, V.305, P.306 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.142, B:E.142

2 x GOL: GLYCEROL

GOL.5: 5 residues within 4Å: Chain A: P.249, Q.250, S.335, W.340, Q.344 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.249, A:S.335, A:Q.344 GOL.15: 5 residues within 4Å: Chain B: P.249, Q.250, S.335, W.340, Q.344 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.344

4 x PO4: PHOSPHATE ION

PO4.8: 4 residues within 4Å: Chain A: R.218, R.405, H.430, R.433 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.433 Water bridges: A:R.218, A:R.218, A:R.218, A:R.405 Salt bridges: A:R.218, A:R.405, A:H.430 PO4.16: 4 residues within 4Å: Chain B: R.218, R.405, H.430, R.433 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.433 Water bridges: B:H.430 Salt bridges: B:R.218, B:R.405, B:H.430 PO4.24: 4 residues within 4Å: Chain C: R.218, R.405, H.430, R.433 6 PLIP interactions: 6 interactions with chain C Water bridges: C:R.433, C:R.433 Salt bridges: C:R.218, C:R.405, C:H.430, C:R.433 PO4.32: 4 residues within 4Å: Chain D: R.218, R.405, H.430, R.433 7 PLIP interactions: 7 interactions with chain D Water bridges: D:R.218, D:H.430, D:R.433 Salt bridges: D:R.218, D:R.405, D:H.430, D:R.433

4 x MG: MAGNESIUM ION

MG.9: 4 residues within 4Å: Chain A: D.441, N.468, G.470 Ligands: TPP.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.441, A:G.470, H2O.2 MG.17: 5 residues within 4Å: Chain B: D.441, N.468, G.470, G.472 Ligands: TPP.12 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.441, B:G.470, H2O.12 MG.25: 5 residues within 4Å: Chain C: D.441, N.468, G.470, G.472 Ligands: TPP.20 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.441, C:G.470, H2O.20 MG.33: 5 residues within 4Å: Chain D: D.441, N.468, G.470, G.472 Ligands: TPP.29 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.441, D:G.470, H2O.28

5 x CL: CHLORIDE ION

CL.10: 3 residues within 4Å: Chain A: H.430, D.432, R.433 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain B: W.89, S.90, N.92, R.272 Ligand excluded by PLIP CL.26: 5 residues within 4Å: Chain C: S.237, P.238, R.256, M.277, R.396 Ligand excluded by PLIP CL.27: 4 residues within 4Å: Chain C: W.89, S.90, N.92, R.272 Ligand excluded by PLIP CL.34: 4 residues within 4Å: Chain D: W.89, S.90, N.92, R.272 Ligand excluded by PLIP

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
C

D
D

Oxalyl-CoA decarboxylase

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