SMTL ID : 8vze.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-tetramer

Ligands

4 x 01: 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-(hydroxymethyl)-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium

01.1: 27 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, F.112, Q.113 Ligands: COA.2, MG.4 24 PLIP interactions: 20 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:F.446, A:F.446, A:I.471, C:I.25, C:V.73 Hydrogen bonds: A:A.389, A:S.390, A:S.390, A:T.391, A:T.391, A:G.414, A:M.416, A:D.441, A:S.442, A:A.443, A:N.468, A:N.468, A:G.472, A:G.473, C:Q.113 Water bridges: A:S.390, A:T.391, A:N.468, C:I.28 01.14: 26 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 Chain D: I.25, V.26, E.50, V.73, P.76, G.77, H.80, Q.113 Ligands: COA.8, MG.10 24 PLIP interactions: 20 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: B:F.446, B:F.446, B:I.471, D:I.25, D:V.73 Hydrogen bonds: B:Y.367, B:A.389, B:S.390, B:S.390, B:T.391, B:G.414, B:M.416, B:D.441, B:S.442, B:A.443, B:N.468, B:N.468, B:G.472, B:G.473, D:Q.113 Water bridges: B:S.390, B:T.391, B:T.391, D:E.50 01.15: 27 residues within 4Å: Chain A: I.25, V.26, E.50, V.73, P.76, G.77, H.80, F.112, 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: COA.16, MG.18 26 PLIP interactions: 5 interactions with chain A, 21 interactions with chain C Hydrophobic interactions: A:I.25, A:V.73, C:F.446, C:F.446, C:I.471 Hydrogen bonds: A:Q.113, C:Y.367, C:A.389, C:S.390, C:S.390, C:T.391, C:G.414, C:M.416, C:D.441, C:D.441, C:S.442, C:A.443, C:N.468, C:N.468, C:G.472, C:G.473 Water bridges: A:I.28, A:E.50, C:S.390, C:T.391, C:T.391 01.28: 26 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 Ligands: COA.22, MG.24 22 PLIP interactions: 3 interactions with chain B, 19 interactions with chain D Hydrophobic interactions: B:I.25, B:V.73, D:F.446, D:F.446, D:I.471 Hydrogen bonds: B:Q.113, D:A.389, D:S.390, 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, D:G.473 Water bridges: D:S.390, D:T.391, D:N.468

4 x COA: COENZYME A

COA.2: 22 residues within 4Å: Chain A: P.238, A.253, A.254, A.255, R.256, S.257, W.275, M.276, H.278, N.350, G.388, M.392, D.393, R.396, T.397, G.414, M.416, K.541, Q.543, W.547 Chain C: F.112 Ligands: 01.1 25 PLIP interactions: 24 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:W.275, A:W.275, A:W.547, C:F.112 Hydrogen bonds: A:A.253, A:R.256, A:S.257, A:S.257, A:N.350, A:R.396, A:T.397, A:Q.543 Water bridges: A:R.256, A:F.258, A:R.284, A:R.284, A:D.393, A:T.397, A:Q.543, A:E.544, A:W.547 Salt bridges: A:R.256, A:R.256, A:R.396, A:K.541 COA.8: 23 residues within 4Å: Chain B: P.238, A.253, A.254, A.255, R.256, S.257, W.275, M.276, H.278, N.350, V.354, G.388, M.392, D.393, R.396, T.397, G.414, M.416, K.541, Q.543, W.547 Chain D: F.112 Ligands: 01.14 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:W.275, B:W.275, B:W.547 Hydrogen bonds: B:A.253, 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:F.258, B:R.284, B:D.393, B:T.397, B:Q.543 Salt bridges: B:R.256, B:R.256, B:R.396, B:R.396, B:K.541 COA.16: 22 residues within 4Å: Chain A: F.112 Chain C: P.238, A.253, A.254, A.255, R.256, S.257, W.275, M.276, H.278, N.350, G.388, M.392, D.393, R.396, T.397, G.414, M.416, K.541, Q.543, W.547 Ligands: 01.15 24 PLIP interactions: 23 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:W.275, C:W.275, C:W.547, A:F.112 Hydrogen bonds: C:A.253, C:R.256, C:S.257, C:S.257, C:N.350, C:R.396, C:T.397, C:Q.543 Water bridges: C:R.256, C:F.258, C:R.284, C:R.284, C:D.393, C:Q.543, C:E.544, C:W.547 Salt bridges: C:R.256, C:R.256, C:R.396, C:K.541 COA.22: 23 residues within 4Å: Chain B: F.112 Chain D: P.238, A.253, A.254, A.255, R.256, S.257, W.275, M.276, H.278, N.350, V.354, G.388, M.392, D.393, R.396, T.397, G.414, M.416, K.541, Q.543, W.547 Ligands: 01.28 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:W.275, D:W.275, D:W.547 Hydrogen bonds: D:A.253, 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:F.258, D:R.284, D:D.393, D:T.397, D:Q.543 Salt bridges: D:R.256, D:R.256, D:R.396, D:R.396, D:K.541

4 x ADP: ADENOSINE-5'-DIPHOSPHATE

ADP.3: 20 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 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: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:M.239, A:N.274, A:T.412 Salt bridges: A:K.212, A:K.212, A:R.272 ADP.9: 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 21 PLIP interactions: 21 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, B:T.412 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.17: 20 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 19 PLIP interactions: 19 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:S.237, C:R.272, C:R.272, C:N.274, C:I.296, C:D.314, C:A.315 Water bridges: C:M.239, C:N.274, C:T.412 Salt bridges: C:K.212, C:K.212, C:R.272 ADP.23: 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 Water bridges: D:S.237, D:M.239, D:N.274, D:T.412, D:T.412 Salt bridges: D:K.212, D:K.212, D:R.272

4 x MG: MAGNESIUM ION

MG.4: 4 residues within 4Å: Chain A: D.441, N.468, G.470 Ligands: 01.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.441, A:G.470, H2O.3 MG.10: 4 residues within 4Å: Chain B: D.441, N.468, G.470 Ligands: 01.14 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.441, B:G.470, H2O.22 MG.18: 4 residues within 4Å: Chain C: D.441, N.468, G.470 Ligands: 01.15 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.441, C:G.470, H2O.39 MG.24: 4 residues within 4Å: Chain D: D.441, N.468, G.470 Ligands: 01.28 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.441, D:G.470, H2O.58

12 x EDO: 1,2-ETHANEDIOL

EDO.5: 4 residues within 4Å: Chain A: W.89, S.90, N.92, R.272 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.90, A:N.92, A:R.272, A:R.272 Water bridges: A:W.89 EDO.6: 7 residues within 4Å: Chain A: G.302, N.304, V.305, P.306 Chain B: F.139, E.142, P.177 2 PLIP interactions: 2 interactions with chain B Water bridges: B:F.139, B:E.142 EDO.7: 6 residues within 4Å: Chain A: N.467, N.469, D.476, M.533, I.534, N.536 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.467, A:D.476, A:I.534 Water bridges: A:Q.491 EDO.11: 7 residues within 4Å: Chain A: F.139, E.142, P.177 Chain B: G.302, N.304, V.305, P.306 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.142 EDO.12: 5 residues within 4Å: Chain B: Y.127, A.128, A.129 Chain C: G.108, E.114 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:A.128 Water bridges: B:R.122, B:Y.140, C:N.107, C:G.108 EDO.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.19: 4 residues within 4Å: Chain C: W.89, S.90, N.92, R.272 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.90, C:N.92, C:R.272, C:R.272 Water bridges: C:W.89 EDO.20: 7 residues within 4Å: Chain C: G.302, N.304, V.305, P.306 Chain D: F.139, E.142, P.177 2 PLIP interactions: 2 interactions with chain D Water bridges: D:F.139, D:E.142 EDO.21: 6 residues within 4Å: Chain C: N.467, N.469, D.476, M.533, I.534, N.536 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.467, C:D.476, C:I.534 Water bridges: C:Q.491 EDO.25: 7 residues within 4Å: Chain C: F.139, E.142, P.177 Chain D: G.302, N.304, V.305, P.306 No protein-ligand interaction detected (PLIP) EDO.26: 5 residues within 4Å: Chain A: G.108, E.114 Chain D: Y.127, A.128, A.129 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:A.128 Water bridges: D:R.122, D:Y.140, D:Y.140, A:G.108 EDO.27: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (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
A

D
B

Oxalyl-CoA decarboxylase

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