SMTL ID : 8vzk.1

Crystal Structure of 2-Hydroxyacyl-CoA Lyase/Synthase CfhHACS from Chloroflexi bacterium in the Complex with THDP and ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-tetramer

Ligands

4 x TPP: THIAMINE DIPHOSPHATE

TPP.1: 27 residues within 4Å: Chain A: Y.372, G.393, A.394, S.395, T.396, G.419, S.420, M.421, G.445, D.446, G.447, A.448, F.451, N.473, G.475, I.476, G.477, R.546 Chain B: V.30, V.31, E.55, V.78, P.81, G.82, N.85, Q.118 Ligands: MG.3 19 PLIP interactions: 15 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.451, B:V.30, B:V.78, B:P.81 Hydrogen bonds: A:Y.372, A:A.394, A:S.395, A:T.396, A:T.396, A:G.419, A:M.421, A:G.445, A:G.447, A:A.448, A:N.473, A:N.473, A:G.477, B:Q.118 Salt bridges: A:R.546 TPP.7: 27 residues within 4Å: Chain A: V.30, V.31, E.55, V.78, P.81, G.82, N.85, Q.118 Chain B: Y.372, G.393, A.394, S.395, T.396, G.419, S.420, M.421, G.445, D.446, G.447, A.448, F.451, N.473, G.475, I.476, G.477, R.546 Ligands: MG.9 18 PLIP interactions: 14 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.476, A:V.30, A:V.78, A:P.81 Hydrogen bonds: B:Y.372, B:A.394, B:S.395, B:T.396, B:T.396, B:G.419, B:M.421, B:G.445, B:G.447, B:A.448, B:N.473, B:G.477, A:Q.118 Salt bridges: B:R.546 TPP.11: 27 residues within 4Å: Chain C: Y.372, G.393, A.394, S.395, T.396, G.419, S.420, M.421, G.445, D.446, G.447, A.448, F.451, N.473, G.475, I.476, G.477, R.546 Chain D: V.30, V.31, E.55, V.78, P.81, G.82, N.85, Q.118 Ligands: MG.13 17 PLIP interactions: 13 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:F.451, D:V.30, D:V.78, D:P.81 Hydrogen bonds: C:A.394, C:S.395, C:T.396, C:G.419, C:M.421, C:G.445, C:D.446, C:G.447, C:A.448, C:N.473, C:G.477, D:Q.118 Salt bridges: C:R.546 TPP.17: 27 residues within 4Å: Chain C: V.30, V.31, E.55, V.78, P.81, G.82, N.85, Q.118 Chain D: Y.372, G.393, A.394, S.395, T.396, G.419, S.420, M.421, G.445, D.446, G.447, A.448, F.451, N.473, G.475, I.476, G.477, R.546 Ligands: MG.19 16 PLIP interactions: 12 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:I.476, C:V.30, C:V.78, C:P.81 Hydrogen bonds: D:A.394, D:S.395, D:T.396, D:G.419, D:M.421, D:G.445, D:D.446, D:G.447, D:A.448, D:G.477, C:Q.118 Salt bridges: D:R.546

4 x ADP: ADENOSINE-5'-DIPHOSPHATE

ADP.2: 18 residues within 4Å: Chain A: G.216, K.217, G.218, A.221, S.222, M.242, G.275, A.276, R.277, M.281, D.300, F.301, N.302, E.305, G.318, D.319, A.320, S.417 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:K.217, A:R.277, A:R.277, A:N.279, A:F.301, A:N.302, A:E.305, A:D.319, A:D.319, A:A.320, A:S.417, A:S.417 Salt bridges: A:K.217, A:K.217, A:R.277 pi-Stacking: A:F.301, A:F.301 ADP.8: 17 residues within 4Å: Chain B: G.216, K.217, G.218, S.222, M.242, G.275, A.276, R.277, N.279, M.281, D.300, F.301, N.302, G.318, D.319, A.320, S.417 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:K.217, B:R.277, B:R.277, B:N.279, B:F.301, B:N.302, B:D.319, B:D.319, B:A.320, B:S.417, B:S.417 Salt bridges: B:K.217, B:K.217, B:R.277 pi-Stacking: B:F.301, B:F.301 ADP.12: 18 residues within 4Å: Chain C: G.216, K.217, G.218, A.221, S.222, M.242, G.275, A.276, R.277, M.281, D.300, F.301, N.302, E.305, G.318, D.319, A.320, S.417 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:K.217, C:R.277, C:R.277, C:N.279, C:F.301, C:N.302, C:D.319, C:A.320, C:S.417, C:S.417 Salt bridges: C:K.217, C:K.217, C:R.277 pi-Stacking: C:F.301, C:F.301 ADP.18: 17 residues within 4Å: Chain D: G.216, K.217, G.218, S.222, M.242, G.275, A.276, R.277, N.279, M.281, D.300, F.301, N.302, G.318, D.319, A.320, S.417 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:K.217, D:R.277, D:R.277, D:N.279, D:F.301, D:N.302, D:D.319, D:A.320, D:S.417, D:S.417 Salt bridges: D:K.217, D:K.217, D:R.277 pi-Stacking: D:F.301, D:F.301

4 x MG: MAGNESIUM ION

MG.3: 5 residues within 4Å: Chain A: D.446, F.471, N.473, G.475 Ligands: TPP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.446, A:G.475 MG.9: 5 residues within 4Å: Chain B: D.446, F.471, N.473, G.475 Ligands: TPP.7 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.446 MG.13: 5 residues within 4Å: Chain C: D.446, F.471, N.473, G.475 Ligands: TPP.11 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.446, C:G.475 MG.19: 5 residues within 4Å: Chain D: D.446, F.471, N.473, G.475 Ligands: TPP.17 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.446

6 x EDO: 1,2-ETHANEDIOL

EDO.4: 2 residues within 4Å: Chain A: E.176, S.177 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.176, A:S.177 EDO.5: 1 residues within 4Å: Chain A: D.254 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.254 EDO.10: 4 residues within 4Å: Chain B: E.176, S.177, V.179, W.181 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.177 EDO.14: 2 residues within 4Å: Chain C: E.176, S.177 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.176, C:S.177 EDO.15: 1 residues within 4Å: Chain C: D.254 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.254 EDO.20: 4 residues within 4Å: Chain D: E.176, S.177, V.179, W.181 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.177

2 x PEG: DI(HYDROXYETHYL)ETHER

PEG.6: 7 residues within 4Å: Chain A: G.156, F.301, P.303 Chain D: G.156, V.157, F.301, P.303 No protein-ligand interaction detected (PLIP) PEG.16: 7 residues within 4Å: Chain B: G.156, V.157, F.301, P.303 Chain C: G.156, F.301, P.303 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