SMTL ID : 8i01.1 (1 other biounit)

Crystal structure of Escherichia coli glyoxylate carboligase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 35 residues within 4Å: Chain A: S.95, R.155, P.156, G.212, G.213, G.214, N.217, A.218, T.238, L.239, M.240, V.256, G.257, L.258, Q.259, T.260, G.279, N.280, R.281, A.283, R.285, H.286, D.303, I.304, E.305, Q.308, S.321, D.322, A.323, I.394, Q.398, I.399, G.417, Q.418 Chain C: F.115 32 PLIP interactions: 31 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:L.239, A:Q.259, A:T.260, A:I.394, A:I.399, C:F.115 Hydrogen bonds: A:R.155, A:G.213, A:G.214, A:T.238, A:T.238, A:L.239, A:V.256, A:L.258, A:Q.259, A:T.260, A:R.281, A:R.281, A:I.304, A:Q.308, A:D.322, A:A.323, A:G.417 Water bridges: A:A.93, A:D.94, A:D.94, A:R.155, A:N.217, A:N.280, A:A.283 Salt bridges: A:R.281, A:R.281 FAD.7: 36 residues within 4Å: Chain B: S.95, R.155, P.156, K.186, G.212, G.213, G.214, N.217, A.218, T.238, L.239, M.240, V.256, G.257, L.258, Q.259, T.260, G.279, N.280, R.281, A.283, R.285, H.286, D.303, I.304, E.305, Q.308, S.321, D.322, A.323, I.394, Q.398, I.399, G.417, Q.418 Chain D: F.115 35 PLIP interactions: 34 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:L.239, B:Q.259, B:T.260, B:I.394, B:I.394, B:I.399, D:F.115 Hydrogen bonds: B:R.155, B:K.186, B:G.213, B:G.214, B:T.238, B:L.239, B:V.256, B:L.258, B:Q.259, B:T.260, B:T.260, B:R.281, B:R.281, B:H.286, B:I.304, B:Q.308, B:D.322, B:D.322, B:A.323, B:G.417 Water bridges: B:A.93, B:D.94, B:R.155, B:N.217, B:N.280, B:A.283 Salt bridges: B:R.281, B:R.281 FAD.13: 35 residues within 4Å: Chain A: F.115 Chain C: S.95, R.155, P.156, G.212, G.213, G.214, N.217, A.218, T.238, L.239, M.240, V.256, G.257, L.258, Q.259, T.260, G.279, N.280, R.281, A.283, R.285, H.286, D.303, I.304, E.305, Q.308, S.321, D.322, A.323, I.394, Q.398, I.399, G.417, Q.418 33 PLIP interactions: 32 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.239, C:Q.259, C:T.260, C:I.394, C:I.399, A:F.115 Hydrogen bonds: C:R.155, C:G.213, C:G.214, C:T.238, C:L.239, C:V.256, C:L.258, C:Q.259, C:T.260, C:T.260, C:R.281, C:R.281, C:H.286, C:I.304, C:Q.308, C:D.322, C:D.322, C:A.323, C:G.417 Water bridges: C:A.93, C:D.94, C:R.155, C:N.217, C:N.280, C:A.283 Salt bridges: C:R.281, C:R.281 FAD.19: 36 residues within 4Å: Chain B: F.115 Chain D: S.95, R.155, P.156, K.186, G.212, G.213, G.214, N.217, A.218, T.238, L.239, M.240, V.256, G.257, L.258, Q.259, T.260, G.279, N.280, R.281, A.283, R.285, H.286, D.303, I.304, E.305, Q.308, S.321, D.322, A.323, I.394, Q.398, I.399, G.417, Q.418 34 PLIP interactions: 33 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:L.239, D:Q.259, D:T.260, D:I.394, D:I.394, D:I.399, B:F.115 Hydrogen bonds: D:R.155, D:K.186, D:G.213, D:G.214, D:T.238, D:T.238, D:L.239, D:V.256, D:L.258, D:Q.259, D:T.260, D:R.281, D:R.281, D:I.304, D:Q.308, D:D.322, D:A.323, D:G.417 Water bridges: D:A.93, D:D.94, D:D.94, D:R.155, D:N.217, D:N.280, D:A.283 Salt bridges: D:R.281, D:R.281

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)(Covalent)

TPP.2: 26 residues within 4Å: Chain A: I.394, G.395, L.396, S.397, G.420, L.422, G.446, D.447, F.448, D.449, F.452, N.474, Y.476, L.477, G.478, L.479, I.480 Chain C: V.26, P.27, V.52, T.76, P.79, A.80, D.83, Q.116 Ligands: MG.3 23 PLIP interactions: 19 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:F.448, A:F.452, A:L.477, A:L.477, A:I.480, C:V.26, C:V.52, C:T.76 Hydrogen bonds: A:L.396, A:S.397, A:G.420, A:L.422, A:G.446, A:F.448, A:D.449, A:N.474, A:G.478, A:L.479, C:Q.116 Water bridges: A:S.397, A:D.447, A:D.449, A:N.474 TPP.8: 27 residues within 4Å: Chain B: I.394, G.395, L.396, S.397, G.420, P.421, L.422, G.446, D.447, F.448, D.449, F.452, N.474, Y.476, L.477, G.478, L.479, I.480 Chain D: V.26, P.27, V.52, T.76, P.79, A.80, D.83, Q.116 Ligands: MG.9 24 PLIP interactions: 5 interactions with chain D, 19 interactions with chain B Hydrophobic interactions: D:V.26, D:V.52, D:T.76, D:D.83, B:F.448, B:F.452, B:L.477, B:L.477 Hydrogen bonds: D:Q.116, B:L.396, B:S.397, B:S.397, B:G.420, B:L.422, B:G.446, B:F.448, B:D.449, B:N.474, B:Y.476, B:G.478, B:L.479 Water bridges: B:S.397, B:D.447, B:D.447 TPP.14: 26 residues within 4Å: Chain A: V.26, P.27, V.52, T.76, P.79, A.80, D.83, Q.116 Chain C: I.394, G.395, L.396, S.397, G.420, L.422, G.446, D.447, F.448, D.449, F.452, N.474, Y.476, L.477, G.478, L.479, I.480 Ligands: MG.15 22 PLIP interactions: 18 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:F.448, C:F.452, C:L.477, C:L.477, C:I.480, A:V.26, A:V.52, A:T.76 Hydrogen bonds: C:L.396, C:S.397, C:G.420, C:L.422, C:G.446, C:F.448, C:D.449, C:G.478, C:L.479, A:Q.116 Water bridges: C:S.397, C:D.447, C:N.474, C:N.474 TPP.20: 27 residues within 4Å: Chain B: V.26, P.27, V.52, T.76, P.79, A.80, D.83, Q.116 Chain D: I.394, G.395, L.396, S.397, G.420, P.421, L.422, G.446, D.447, F.448, D.449, F.452, N.474, Y.476, L.477, G.478, L.479, I.480 Ligands: MG.21 24 PLIP interactions: 5 interactions with chain B, 19 interactions with chain D Hydrophobic interactions: B:V.26, B:V.52, B:T.76, B:D.83, D:F.448, D:F.452, D:L.477, D:L.477 Hydrogen bonds: B:Q.116, D:L.396, D:S.397, D:S.397, D:G.420, D:L.422, D:G.446, D:F.448, D:D.449, D:N.474, D:Y.476, D:G.478, D:L.479 Water bridges: D:S.397, D:D.447, D:D.447

8 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.447, N.474, Y.476 Ligands: TPP.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.447, A:Y.476, H2O.4 MG.4: 7 residues within 4Å: Chain A: F.452, L.453, E.455 Chain C: F.452, L.453, E.455 Ligands: MG.16 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Metal complexes: A:F.452, A:E.455, C:F.452, C:E.455 MG.9: 4 residues within 4Å: Chain B: D.447, N.474, Y.476 Ligands: TPP.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.447, B:Y.476, H2O.27 MG.10: 7 residues within 4Å: Chain B: F.452, L.453, E.455 Chain D: F.452, L.453, E.455 Ligands: MG.22 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D Metal complexes: B:F.452, B:E.455, D:F.452, D:E.455 MG.15: 4 residues within 4Å: Chain C: D.447, N.474, Y.476 Ligands: TPP.14 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.447, C:Y.476, H2O.43 MG.16: 7 residues within 4Å: Chain A: F.452, L.453, E.455 Chain C: F.452, L.453, E.455 Ligands: MG.4 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Metal complexes: A:F.452, A:E.455, C:F.452, C:E.455 MG.21: 4 residues within 4Å: Chain D: D.447, N.474, Y.476 Ligands: TPP.20 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.447, D:Y.476, H2O.66 MG.22: 7 residues within 4Å: Chain B: F.452, L.453, E.455 Chain D: F.452, L.453, E.455 Ligands: MG.10 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Metal complexes: D:F.452, D:E.455, B:F.452, B:E.455

8 x UQ0: 2,3-DIMETHOXY-5-METHYL-1,4-BENZOQUINONE(Covalent)(Non-covalent)

UQ0.5: 3 residues within 4Å: Chain A: Q.354, R.358, C.589 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.358 Water bridges: A:K.357 UQ0.6: 5 residues within 4Å: Chain A: C.492, V.493, Q.494 Chain C: H.46, Q.462 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Water bridges: A:C.492, A:C.492 Hydrogen bonds: C:H.46, C:Q.462 pi-Stacking: C:F.463 UQ0.11: 3 residues within 4Å: Chain B: Q.354, R.358, C.589 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.358 UQ0.12: 6 residues within 4Å: Chain B: C.492, V.493, Q.494 Chain D: H.46, L.48, Q.462 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.462 UQ0.17: 3 residues within 4Å: Chain C: Q.354, R.358, C.589 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:R.358 Water bridges: C:K.357 UQ0.18: 5 residues within 4Å: Chain A: H.46, Q.462 Chain C: C.492, V.493, Q.494 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Water bridges: C:C.492, C:C.492 Hydrogen bonds: A:Q.462 pi-Stacking: A:F.463 UQ0.23: 3 residues within 4Å: Chain D: Q.354, R.358, C.589 No protein-ligand interaction detected (PLIP) UQ0.24: 6 residues within 4Å: Chain B: H.46, L.48, Q.462 Chain D: C.492, V.493, Q.494 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.46, B:Q.462

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, J.H. et al., Engineering of two thiamine diphosphate-dependent enzymes for the regioselective condensation of C1-formaldehyde into C4-erythrulose. Int.J.Biol.Macromol. (2023)

Release Date

2023-11-22

Peptides

Glyoxylate carboligase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Glyoxylate carboligase

Related Entries With Identical Sequence