SMTL ID : 8vzd.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x TPP: THIAMINE DIPHOSPHATE

TPP.1: 26 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 C: I.25, V.26, E.50, V.73, P.76, G.77, H.80, Q.113 Ligands: FYN.2, CA.3 21 PLIP interactions: 16 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:I.471, A:I.471, C:I.25, C:V.73, C:P.76 Hydrogen bonds: A:A.389, A:S.390, A:T.391, A:T.391, A:G.414, A:M.416, A:G.440, A:S.442, A:A.443, A:N.468, A:G.472, A:G.473, C:Q.113 Water bridges: A:D.441, A:N.468, C:V.73 TPP.10: 27 residues within 4Å: 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 Chain D: I.25, V.26, E.50, V.73, P.76, G.77, H.80, Q.113 Ligands: FYN.11, CA.12 21 PLIP interactions: 17 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: B:I.471, B:I.471, D:I.25, D:V.73, D:P.76 Hydrogen bonds: B:Y.367, B:A.389, B:S.390, B:T.391, B:G.414, B:M.416, B:G.440, B:S.442, B:A.443, B:N.468, B:N.468, B:G.472, B:G.473, D:Q.113 Water bridges: B:T.391, B:D.441 TPP.18: 26 residues within 4Å: Chain A: I.25, V.26, E.50, V.73, P.76, G.77, H.80, Q.113 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 Ligands: FYN.19, CA.20 22 PLIP interactions: 5 interactions with chain A, 17 interactions with chain C Hydrophobic interactions: A:I.25, A:V.73, A:P.76, C:I.471, C:I.471 Hydrogen bonds: A:Q.113, C:Y.367, C:A.389, C:S.390, C:T.391, C:G.414, C:M.416, C:G.440, C:S.442, C:A.443, C:N.468, C:N.468, C:G.472, C:G.473 Water bridges: A:V.73, C:D.441, C:N.468 TPP.27: 27 residues within 4Å: Chain B: 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, G.473 Ligands: FYN.28, CA.29 21 PLIP interactions: 17 interactions with chain D, 4 interactions with chain B Hydrophobic interactions: D:I.471, D:I.471, B:I.25, B:V.73, B:P.76 Hydrogen bonds: D:A.389, D:S.390, D:T.391, D:T.391, D:G.414, D:M.416, D:G.440, D:S.442, D:A.443, D:N.468, D:N.468, D:G.472, D:G.473, B:Q.113 Water bridges: D:D.441, D:D.441

4 x FYN: S-{(9R,13S,15R)-17-[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]-9,13,15-TRIHYDROXY-10,10-DIMETHYL-13,15-DIOXIDO-4,8-DIOXO-12,14,16-TRIOXA-3,7-DIAZA-13,15-DIPHOSPHAHEPTADEC-1-YL} THIOFORMATE

FYN.2: 23 residues within 4Å: Chain A: P.238, A.253, A.254, A.255, R.256, S.257, W.275, M.276, N.350, A.351, V.354, G.388, M.392, D.393, R.396, T.397, G.414, K.541, Q.543, W.547 Chain C: I.28, F.112 Ligands: TPP.1 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:W.275, A:W.275, A:W.547 Hydrogen bonds: A:A.253, A:R.256, A:S.257, A:S.257, A:N.350, A:R.396, A:R.396, A:Q.543 Water bridges: A:A.255, A:R.256, A:F.258, A:R.284, A:D.393, A:T.397, A:T.397, A:W.547 Salt bridges: A:R.256, A:R.256, A:R.396, A:R.396, A:K.541 FYN.11: 23 residues within 4Å: Chain B: P.238, A.253, A.254, A.255, R.256, S.257, W.275, M.276, N.350, V.354, G.388, M.392, D.393, R.396, T.397, G.414, K.541, Q.543, W.547 Chain D: I.28, F.112 Ligands: TPP.10, EDO.16 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:W.275, B:W.275, B:W.547 Hydrogen bonds: B:A.254, B:R.256, B:S.257, B:S.257, B:N.350, B:R.396, B:R.396, B:Q.543 Water bridges: B:R.256, B:R.284, B:Y.368, B:D.393, B:T.397 Salt bridges: B:R.256, B:R.256, B:R.396, B:R.396, B:K.541 FYN.19: 23 residues within 4Å: Chain A: I.28, F.112 Chain C: P.238, A.253, A.254, A.255, R.256, S.257, W.275, M.276, N.350, A.351, V.354, G.388, M.392, D.393, R.396, T.397, G.414, K.541, Q.543, W.547 Ligands: TPP.18 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:W.275, C:W.275, C:W.547 Hydrogen bonds: C:A.253, C:R.256, C:S.257, C:S.257, C:N.350, C:R.396, C:R.396, C:Q.543 Water bridges: C:A.255, C:R.256, C:F.258, C:R.284, C:D.393, C:T.397, C:W.547 Salt bridges: C:R.256, C:R.256, C:R.396, C:R.396, C:K.541 FYN.28: 23 residues within 4Å: Chain B: I.28, F.112 Chain D: P.238, A.253, A.254, A.255, R.256, S.257, W.275, M.276, N.350, V.354, G.388, M.392, D.393, R.396, T.397, G.414, K.541, Q.543, W.547 Ligands: TPP.27, EDO.33 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:W.275, D:W.275, D:W.547 Hydrogen bonds: D:A.254, D:R.256, D:S.257, D:S.257, D:N.350, D:R.396, D:R.396, D:Q.543 Water bridges: D:R.256, D:R.284, D:D.393, D:T.397, D:T.397 Salt bridges: D:R.256, D:R.256, D:R.396, D:R.396, D:K.541

4 x CA: CALCIUM ION

CA.3: 4 residues within 4Å: Chain A: D.441, N.468, G.470 Ligands: TPP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.441, A:G.470, H2O.2 CA.12: 5 residues within 4Å: Chain B: D.441, N.468, G.470, G.472 Ligands: TPP.10 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.441, B:G.470, H2O.13 CA.20: 4 residues within 4Å: Chain C: D.441, N.468, G.470 Ligands: TPP.18 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.441, C:G.470, H2O.21 CA.29: 5 residues within 4Å: Chain D: D.441, N.468, G.470, G.472 Ligands: TPP.27 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.441, D:G.470, H2O.32

4 x ADP: ADENOSINE-5'-DIPHOSPHATE

ADP.4: 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.6 22 PLIP interactions: 22 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:S.297, A:D.314, A:D.314, A:A.315, A:T.412 Water bridges: A:N.92, A:M.239, A:R.272, A:R.272 Salt bridges: A:K.212, A:K.212, A:R.272 ADP.13: 20 residues within 4Å: Chain B: 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 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:R.152, B:R.152, B:K.212, B:S.217, B:S.237, B:S.237, B:R.272, B:R.272, B:N.274, B:I.296, B:D.314, B:D.314, B:A.315 Water bridges: B:S.237, B:M.239, B:N.274, B:T.412 Salt bridges: B:K.212, B:K.212, B:R.272 ADP.21: 21 residues within 4Å: Chain C: 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.23 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:S.297, C:D.314, C:A.315 Water bridges: C:N.92, C:M.239, C:R.272, C:R.272 Salt bridges: C:K.212, C:K.212, C:R.272 ADP.30: 20 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 20 PLIP interactions: 20 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, D:T.412 Water bridges: D:S.237, D:M.239, D:N.274, D:T.412 Salt bridges: D:K.212, D:K.212, D:R.272

16 x EDO: 1,2-ETHANEDIOL

EDO.5: 7 residues within 4Å: Chain A: I.28, S.74, N.102, D.103, Q.106, F.112 Chain C: L.548 Ligand excluded by PLIP EDO.6: 9 residues within 4Å: Chain A: Y.62, N.91, N.92, W.93, P.153, K.212, G.213, Y.216 Ligands: ADP.4 Ligand excluded by PLIP EDO.8: 8 residues within 4Å: Chain A: I.378, P.379, K.380, A.382, I.384, P.400, N.401, F.402 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: N.468, N.469, D.476, M.533, I.534, N.536 Ligand excluded by PLIP EDO.14: 7 residues within 4Å: Chain A: F.139, E.142, P.177 Chain B: G.302, N.304, V.305, P.306 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain B: I.28, N.102, D.103, Q.106 Chain D: L.548 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain B: A.236, S.237, P.238, A.253, R.396 Ligands: FYN.11 Ligand excluded by PLIP EDO.17: 9 residues within 4Å: Chain B: P.364, N.468, N.469, G.474, D.476, M.533, I.534, S.535, N.536 Ligand excluded by PLIP EDO.22: 7 residues within 4Å: Chain A: L.548 Chain C: I.28, S.74, N.102, D.103, Q.106, F.112 Ligand excluded by PLIP EDO.23: 9 residues within 4Å: Chain C: Y.62, N.91, N.92, W.93, P.153, K.212, G.213, Y.216 Ligands: ADP.21 Ligand excluded by PLIP EDO.25: 8 residues within 4Å: Chain C: I.378, P.379, K.380, A.382, I.384, P.400, N.401, F.402 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain C: N.468, N.469, D.476, M.533, I.534, N.536 Ligand excluded by PLIP EDO.31: 7 residues within 4Å: Chain C: F.139, E.142, P.177 Chain D: G.302, N.304, V.305, P.306 Ligand excluded by PLIP EDO.32: 5 residues within 4Å: Chain B: L.548 Chain D: I.28, N.102, D.103, Q.106 Ligand excluded by PLIP EDO.33: 6 residues within 4Å: Chain D: A.236, S.237, P.238, A.253, R.396 Ligands: FYN.28 Ligand excluded by PLIP EDO.34: 9 residues within 4Å: Chain D: P.364, N.468, N.469, G.474, D.476, M.533, I.534, S.535, N.536 Ligand excluded by PLIP

2 x PEG: DI(HYDROXYETHYL)ETHER

PEG.7: 4 residues within 4Å: Chain A: E.182, P.183, R.185, D.314 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.185 PEG.24: 4 residues within 4Å: Chain C: E.182, P.183, R.185, D.314 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.185

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

2-Hydroxyacyl-CoA Lyase/Synthase TbHACS: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

2-Hydroxyacyl-CoA Lyase/Synthase TbHACS

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