SMTL ID : 8vzf.1

Crystal Structure of 2-Hydroxyacyl-CoA Lyase/Synthase ApbHACS from Alphaproteobacteria bacterium in the Complex with THDP, Coenzyme A, and ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

homo-tetramer

Ligands

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.1: 24 residues within 4Å: Chain A: P.247, G.262, G.263, A.264, R.265, S.266, W.284, I.285, H.287, N.359, Q.360, V.363, M.401, D.402, R.405, T.406, G.423, M.425, K.551, Q.553, W.557 Chain B: F.37, F.121 Ligands: TPP.2 20 PLIP interactions: 19 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.285, A:W.557 Hydrogen bonds: A:G.262, A:R.265, A:S.266, A:N.359, A:N.359, A:D.402, A:R.405, A:T.406, A:Q.553, B:F.37 Water bridges: A:R.405, A:Q.407, A:Q.407 Salt bridges: A:R.265, A:R.265, A:R.405, A:R.405, A:K.551 FYN.7: 24 residues within 4Å: Chain A: F.37, F.121 Chain B: P.247, G.262, G.263, A.264, R.265, S.266, W.284, I.285, H.287, N.359, V.363, G.397, M.401, D.402, R.405, T.406, G.423, M.425, K.551, Q.553, W.557 Ligands: TPP.8 24 PLIP interactions: 1 interactions with chain A, 23 interactions with chain B Hydrogen bonds: A:F.37, B:G.263, B:R.265, B:S.266, B:S.266, B:N.359, B:N.359, B:D.402, B:R.405, B:R.405, B:T.406, B:Q.553, B:Q.553 Hydrophobic interactions: B:I.285, B:W.557 Water bridges: B:R.265, B:S.266, B:H.267, B:R.293 Salt bridges: B:R.265, B:R.265, B:R.405, B:R.405, B:K.551 FYN.14: 23 residues within 4Å: Chain C: P.247, G.262, G.263, A.264, R.265, S.266, W.284, I.285, H.287, N.359, V.363, G.397, M.401, D.402, R.405, T.406, G.423, K.551, Q.553, W.557 Chain D: F.37, F.121 Ligands: TPP.15 20 PLIP interactions: 1 interactions with chain D, 19 interactions with chain C Hydrogen bonds: D:F.37, C:G.263, C:R.265, C:S.266, C:S.266, C:N.359, C:D.402, C:R.405, C:R.405, C:T.406, C:Q.553, C:Q.553 Hydrophobic interactions: C:I.285, C:W.557 Water bridges: C:Q.553 Salt bridges: C:R.265, C:R.265, C:R.405, C:R.405, C:K.551 FYN.21: 23 residues within 4Å: Chain C: F.37, F.121 Chain D: P.247, G.262, G.263, A.264, R.265, S.266, W.284, I.285, H.287, N.359, V.363, G.397, M.401, D.402, R.405, T.406, G.423, K.551, Q.553, W.557 Ligands: TPP.22 22 PLIP interactions: 21 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:I.285, D:W.557 Hydrogen bonds: D:G.262, D:R.265, D:S.266, D:N.359, D:N.359, D:D.402, D:R.405, D:R.405, D:T.406, D:Q.553, C:F.37 Water bridges: D:R.265, D:R.293, D:R.293, D:R.550 Salt bridges: D:R.265, D:R.265, D:R.405, D:R.405, D:K.551

4 x TPP: THIAMINE DIPHOSPHATE

TPP.2: 26 residues within 4Å: Chain A: Y.376, G.397, A.398, N.399, T.400, G.423, M.425, G.449, D.450, S.451, A.452, F.455, N.477, G.479, I.480, G.481, M.482 Chain B: I.34, V.35, E.59, V.82, P.85, H.89, Q.122 Ligands: FYN.1, MG.3 21 PLIP interactions: 17 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.455, B:I.34, B:V.82, B:P.85 Hydrogen bonds: A:Y.376, A:A.398, A:N.399, A:T.400, A:T.400, A:T.400, A:G.423, A:M.425, A:G.449, A:S.451, A:A.452, A:N.477, A:G.479, A:G.481, B:Q.122 Water bridges: A:D.450, A:D.450 TPP.8: 25 residues within 4Å: Chain A: V.35, E.59, V.82, P.85, H.89, Q.122 Chain B: Y.376, G.397, A.398, N.399, T.400, G.423, M.425, G.449, D.450, S.451, A.452, F.455, N.477, G.479, I.480, G.481, M.482 Ligands: FYN.7, MG.9 19 PLIP interactions: 15 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:A.398, B:N.399, B:T.400, B:T.400, B:T.400, B:G.423, B:M.425, B:G.449, B:D.450, B:S.451, B:S.451, B:A.452, B:N.477, B:G.479, B:G.481, A:Q.122 Hydrophobic interactions: A:V.82, A:P.85 Water bridges: A:E.59 TPP.15: 24 residues within 4Å: Chain C: Y.376, G.397, A.398, N.399, T.400, G.423, M.425, G.449, D.450, S.451, A.452, F.455, N.477, G.479, I.480, G.481 Chain D: V.35, E.59, V.82, P.85, H.89, Q.122 Ligands: FYN.14, MG.16 20 PLIP interactions: 3 interactions with chain D, 17 interactions with chain C Hydrophobic interactions: D:V.82, D:P.85, C:F.455 Hydrogen bonds: D:Q.122, C:A.398, C:N.399, C:T.400, C:T.400, C:G.423, C:M.425, C:G.449, C:D.450, C:S.451, C:S.451, C:A.452, C:N.477, C:G.479, C:G.481 Water bridges: C:T.400, C:T.400 TPP.22: 26 residues within 4Å: Chain C: I.34, V.35, E.59, V.82, P.85, H.89, Q.122 Chain D: Y.376, G.397, A.398, N.399, T.400, G.423, M.425, G.449, D.450, S.451, A.452, F.455, N.477, G.479, I.480, G.481, M.482 Ligands: FYN.21, MG.23 20 PLIP interactions: 16 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:Y.376, D:A.398, D:N.399, D:T.400, D:T.400, D:G.423, D:M.425, D:G.449, D:D.450, D:S.451, D:S.451, D:A.452, D:N.477, D:G.481, C:Q.122 Water bridges: D:T.400, D:T.400 Hydrophobic interactions: C:I.34, C:V.82, C:P.85

4 x MG: MAGNESIUM ION

MG.3: 5 residues within 4Å: Chain A: D.450, N.477, G.479, G.481 Ligands: TPP.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.450, A:G.479, H2O.1 MG.9: 4 residues within 4Å: Chain B: D.450, N.477, G.479 Ligands: TPP.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.450, B:G.479, H2O.5 MG.16: 4 residues within 4Å: Chain C: D.450, N.477, G.479 Ligands: TPP.15 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.450, C:G.479, H2O.8 MG.23: 5 residues within 4Å: Chain D: D.450, N.477, G.479, G.481 Ligands: TPP.22 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.450, D:G.479, H2O.11

4 x ADP: ADENOSINE-5'-DIPHOSPHATE

ADP.4: 19 residues within 4Å: Chain A: C.101, R.161, G.220, K.221, G.222, W.225, S.226, T.246, G.279, A.280, R.281, I.285, D.304, L.305, S.306, G.322, D.323, G.324, S.421 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:R.161, A:R.161, A:K.221, A:T.246, A:T.246, A:R.281, A:R.281, A:L.305, A:S.306, A:D.323, A:D.323, A:G.324, A:S.421 Water bridges: A:R.281, A:R.281 Salt bridges: A:K.221, A:K.221, A:R.281 ADP.10: 20 residues within 4Å: Chain B: C.101, R.161, G.220, K.221, G.222, W.225, S.226, T.246, G.279, A.280, R.281, N.283, I.285, D.304, L.305, S.306, G.322, D.323, G.324, S.421 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:R.161, B:R.161, B:K.221, B:T.246, B:T.246, B:R.281, B:R.281, B:N.283, B:L.305, B:S.306, B:D.323, B:G.324, B:S.421, B:S.421 Water bridges: B:T.246, B:G.249 Salt bridges: B:K.221, B:K.221, B:R.281 ADP.17: 20 residues within 4Å: Chain C: C.101, R.161, G.220, K.221, G.222, W.225, S.226, T.246, G.279, A.280, R.281, N.283, I.285, D.304, L.305, S.306, G.322, D.323, G.324, S.421 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:R.161, C:R.161, C:K.221, C:S.226, C:R.281, C:R.281, C:N.283, C:L.305, C:S.306, C:D.323, C:G.324, C:S.421 Water bridges: C:M.248, C:R.281, C:N.283 Salt bridges: C:K.221, C:K.221, C:R.281 ADP.24: 20 residues within 4Å: Chain D: C.101, R.161, G.220, K.221, G.222, W.225, S.226, T.246, G.279, A.280, R.281, N.283, I.285, D.304, L.305, S.306, G.322, D.323, G.324, S.421 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:R.161, D:R.161, D:K.221, D:T.246, D:R.281, D:R.281, D:N.283, D:L.305, D:S.306, D:D.323, D:D.323, D:G.324, D:S.421 Water bridges: D:T.246, D:G.249, D:R.281, D:R.281 Salt bridges: D:K.221, D:K.221, D:R.281

6 x EDO: 1,2-ETHANEDIOL

EDO.5: 3 residues within 4Å: Chain A: Q.210, S.211, A.212 No protein-ligand interaction detected (PLIP) EDO.11: 4 residues within 4Å: Chain B: H.439, P.440, G.441, R.442 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.439, B:G.441, B:R.442 EDO.12: 4 residues within 4Å: Chain B: E.237, R.240, H.257, P.258 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.240, B:R.240 EDO.25: 4 residues within 4Å: Chain D: H.439, P.440, G.441, R.442 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.439, D:G.441 EDO.26: 3 residues within 4Å: Chain D: Q.234, R.238, Q.333 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.234, D:R.238, D:S.336, D:S.336 Water bridges: D:Q.234 EDO.27: 3 residues within 4Å: Chain D: A.212, Y.342, T.346 No protein-ligand interaction detected (PLIP)

2 x SO4: SULFATE ION

SO4.6: 5 residues within 4Å: Chain A: V.438, H.439, P.440, G.441, R.442 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.441 Water bridges: A:R.442 Salt bridges: A:H.439 SO4.20: 3 residues within 4Å: Chain C: L.290, P.291 Chain D: Q.115 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.115

2 x CL: CHLORIDE ION

CL.13: 2 residues within 4Å: Chain B: L.72, R.227 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain C: R.381, D.382 Ligand excluded by PLIP

1 x GOL: GLYCEROL

GOL.18: 5 residues within 4Å: Chain A: H.138 Chain C: N.116, E.123, E.124, Q.139 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:N.116, C:E.123, C:E.124, C:Q.139, A:H.138 Water bridges: C:Q.126, C:Q.126, A:E.141, A:E.141

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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

2-Hydroxyacyl-CoA Lyase/Synthase