SMTL ID : 8vzi.1

Crystal Structure of 2-Hydroxyacyl-CoA Lyase/Synthase CcHACS from Conidiobolus coronatus in the Complex with THDP and ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 25 residues within 4Å: Chain A: H.365, G.390, A.391, R.392, T.393, G.416, M.418, G.442, D.443, S.444, A.445, F.448, N.470, G.472, I.473, Y.474 Chain B: I.27, V.28, G.29, E.52, V.75, N.82, Q.115 Ligands: ACT.8, MG.10 18 PLIP interactions: 14 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.448, A:I.473, B:I.27, B:V.75 Hydrogen bonds: A:A.391, A:R.392, A:T.393, A:T.393, A:G.416, A:M.418, A:S.444, A:A.445, A:Y.474, B:Q.115 Water bridges: A:D.443, A:N.470, B:E.52 Salt bridges: A:H.365 TPP.12: 24 residues within 4Å: Chain A: I.27, V.28, E.52, V.75, P.78, N.82, Q.115 Chain B: H.365, G.390, A.391, R.392, T.393, G.416, M.418, G.442, D.443, S.444, A.445, F.448, N.470, G.472, I.473, Y.474 Ligands: MG.20 19 PLIP interactions: 4 interactions with chain A, 15 interactions with chain B Hydrophobic interactions: A:I.27, A:V.75, A:P.78, B:F.448, B:I.473 Hydrogen bonds: A:Q.115, B:A.391, B:R.392, B:T.393, B:T.393, B:G.416, B:M.418, B:S.444, B:A.445, B:N.470, B:Y.474 Water bridges: B:D.443, B:N.470 Salt bridges: B:H.365 TPP.22: 25 residues within 4Å: Chain C: H.365, G.390, A.391, R.392, T.393, G.416, M.418, G.442, D.443, S.444, A.445, F.448, N.470, G.472, I.473, Y.474 Chain D: I.27, V.28, E.52, V.75, P.78, N.82, Q.115 Ligands: FMT.28, MG.32 19 PLIP interactions: 4 interactions with chain D, 15 interactions with chain C Hydrophobic interactions: D:I.27, D:V.75, D:P.78, C:F.448, C:I.473 Hydrogen bonds: D:Q.115, C:A.391, C:R.392, C:T.393, C:T.393, C:G.416, C:M.418, C:S.444, C:A.445, C:N.470, C:Y.474 Water bridges: C:D.443, C:N.470 Salt bridges: C:H.365 TPP.33: 26 residues within 4Å: Chain C: I.27, V.28, G.29, E.52, V.75, P.78, N.82, Q.115 Chain D: H.365, G.390, A.391, R.392, T.393, G.416, M.418, G.442, D.443, S.444, A.445, F.448, N.470, G.472, I.473, Y.474 Ligands: EDO.37, MG.39 18 PLIP interactions: 15 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:F.448, D:I.473, C:I.27, C:V.75 Hydrogen bonds: D:A.391, D:R.392, D:T.393, D:T.393, D:G.416, D:M.418, D:S.444, D:A.445, D:N.470, D:Y.474, C:Q.115 Water bridges: D:H.365, D:D.443 Salt bridges: D:H.365

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 19 residues within 4Å: Chain A: R.154, P.155, G.211, K.212, G.213, S.217, T.237, G.270, A.271, R.272, M.276, D.293, I.294, S.295, G.311, N.312, I.313, T.414 Ligands: EDO.3 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:R.154, A:R.154, A:K.212, A:T.237, A:R.272, A:R.272, A:N.274, A:I.294, A:N.312, A:I.313 Water bridges: A:Y.185, A:T.237, A:T.237, A:R.272, A:R.272, A:N.312, A:T.414 Salt bridges: A:K.212, A:K.212, A:R.272 ADP.13: 18 residues within 4Å: Chain B: R.154, G.211, K.212, G.213, S.217, T.237, G.270, A.271, R.272, N.274, M.276, D.293, I.294, S.295, G.311, N.312, I.313, T.414 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:R.154, B:R.154, B:K.212, B:T.237, B:R.272, B:N.274, B:I.294, B:N.312, B:I.313 Water bridges: B:K.212, B:T.237, B:A.240, B:R.272, B:N.312, B:T.414, B:T.414 Salt bridges: B:K.212, B:K.212, B:R.272 ADP.23: 20 residues within 4Å: Chain C: R.154, P.155, Y.185, G.211, K.212, G.213, S.217, T.237, G.270, A.271, R.272, M.276, D.293, I.294, S.295, G.311, N.312, I.313, T.414 Ligands: EDO.24 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:R.154, C:R.154, C:K.212, C:T.237, C:R.272, C:N.274, C:I.294, C:N.312, C:I.313, C:T.414 Water bridges: C:K.212, C:T.237, C:R.272, C:R.272, C:N.274, C:N.312, C:T.414 Salt bridges: C:K.212, C:K.212, C:R.272 ADP.34: 19 residues within 4Å: Chain D: R.154, P.155, Y.185, G.211, K.212, G.213, S.217, T.237, G.270, A.271, R.272, M.276, D.293, I.294, S.295, G.311, N.312, I.313, T.414 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:R.154, D:R.154, D:K.212, D:T.237, D:R.272, D:R.272, D:I.294, D:N.312, D:I.313, D:T.414 Water bridges: D:Y.185, D:T.237, D:A.240, D:R.272, D:R.272, D:N.274 Salt bridges: D:K.212, D:K.212, D:R.272

10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 8 residues within 4Å: Chain A: Y.64, N.93, C.94, W.95, P.155, K.212, Y.216 Ligands: ADP.2 No protein-ligand interaction detected (PLIP) EDO.4: 6 residues within 4Å: Chain A: N.364, H.365, R.392, D.540, R.542, P.543 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.365, A:H.365, A:R.392, A:R.392, A:P.543 EDO.9: 5 residues within 4Å: Chain A: R.205, L.258, K.262, F.336, E.339 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.205, A:K.262 EDO.14: 6 residues within 4Å: Chain B: N.364, H.365, R.392, D.540, R.542, P.543 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.365, B:H.365, B:R.392, B:R.392, B:P.543 EDO.15: 2 residues within 4Å: Chain B: R.256 Ligands: GLY.16 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.253 EDO.24: 9 residues within 4Å: Chain C: Y.64, N.93, C.94, W.95, P.155, K.212, G.213, Y.216 Ligands: ADP.23 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:W.95 EDO.25: 6 residues within 4Å: Chain C: Q.429, P.433, D.434, K.435, K.436, P.462 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.429, C:Q.429, C:K.436 EDO.35: 6 residues within 4Å: Chain D: N.364, H.365, R.392, D.540, R.542, P.543 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:H.365, D:H.365, D:R.392, D:R.392, D:P.543 EDO.37: 7 residues within 4Å: Chain C: F.114 Chain D: G.390, M.394, G.416, M.418, Y.474 Ligands: TPP.33 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.390, D:Y.474 Water bridges: D:Y.474 EDO.38: 3 residues within 4Å: Chain D: A.255, R.256, S.257 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:R.256, D:S.257, D:S.257, D:N.347 Water bridges: D:L.258, D:L.258, D:N.343, D:N.347, D:K.350

3 x ALA: ALANINE(Non-covalent)

ALA.5: 6 residues within 4Å: Chain A: G.253, S.254, A.255, R.256, S.257 Ligands: ALA.7 8 PLIP interactions: 6 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:G.253, A:R.256, A:S.257, A:N.347, A.5, A.5 Water bridges: A:L.258, A:N.343 ALA.6: 5 residues within 4Å: Chain A: S.254, N.347, Q.348, L.351, M.399 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:L.351 Hydrogen bonds: A:S.254, A.6, A.6 ALA.7: 3 residues within 4Å: Chain A: R.256, R.398 Ligands: ALA.5 4 PLIP interactions: 2 Ligand-Ligand interactions, 2 interactions with chain A Hydrogen bonds: A.7, A.7, A:R.256 Salt bridges: A:R.256

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.8: 8 residues within 4Å: Chain A: G.390, A.391, M.394, G.416, M.418, Y.474 Chain B: F.114 Ligands: TPP.1 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Q.115 ACT.29: 3 residues within 4Å: Chain C: R.256, S.257 Ligands: ACT.31 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.257 Water bridges: C:A.255, C:R.256, C:L.258 ACT.31: 2 residues within 4Å: Chain C: R.256 Ligands: ACT.29 3 PLIP interactions: 3 interactions with chain C Water bridges: C:G.253 Salt bridges: C:R.256, C:R.398

4 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 4 residues within 4Å: Chain A: D.443, N.470, G.472 Ligands: TPP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.443, A:G.472, H2O.2 MG.20: 4 residues within 4Å: Chain B: D.443, N.470, G.472 Ligands: TPP.12 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.443, B:G.472, H2O.14 MG.32: 4 residues within 4Å: Chain C: D.443, N.470, G.472 Ligands: TPP.22 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.443, C:G.472, H2O.30 MG.39: 4 residues within 4Å: Chain D: D.443, N.470, G.472 Ligands: TPP.33 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.443, D:G.472, H2O.45

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 2 residues within 4Å: Chain A: R.392, P.543 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain B: R.392, Y.474, P.543 Ligand excluded by PLIP

1 x GLY: GLYCINE(Non-covalent)

GLY.16: 4 residues within 4Å: Chain B: A.255, R.256, S.257 Ligands: EDO.15 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.256, B:S.257 Water bridges: B:L.258, B:L.258

8 x FMT: FORMIC ACID(Non-functional Binders)

FMT.17: 3 residues within 4Å: Chain B: Y.331, S.332, W.333 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.330, B:S.332 Water bridges: B:K.204 FMT.18: 3 residues within 4Å: Chain B: T.356, A.357, Q.367 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.367 FMT.19: 4 residues within 4Å: Chain B: L.258, K.262, F.336, E.339 No protein-ligand interaction detected (PLIP) FMT.26: 3 residues within 4Å: Chain C: L.258, K.262, E.339 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.339 FMT.27: 3 residues within 4Å: Chain C: Y.331, S.332, W.333 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.332 FMT.28: 5 residues within 4Å: Chain C: G.390, M.394, G.416, Y.474 Ligands: TPP.22 1 PLIP interactions: 1 interactions with chain D Water bridges: D:Q.115 FMT.30: 1 residues within 4Å: Chain C: M.276 No protein-ligand interaction detected (PLIP) FMT.36: 3 residues within 4Å: Chain D: Y.331, S.332, W.333 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.332, D:S.332

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-like protein 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

2-hydroxyacyl-CoA lyase-like protein 1