- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.15 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)
- 4 x TPP: THIAMINE DIPHOSPHATE(Non-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
22 PLIP interactions:18 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:N.474
TPP.8: 24 residues within 4Å:- Chain B: 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 D: P.27, V.52, T.76, P.79, D.83, Q.116
- Ligands: MG.9
20 PLIP interactions:17 interactions with chain B, 3 interactions with chain D- Hydrophobic interactions: B:F.452, B:L.477, B:L.477, D:V.52, D:T.76
- Hydrogen bonds: 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:G.478, B:L.479, D:Q.116
- Water bridges: B:S.397, B:D.447, B:N.474
TPP.15: 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.16
24 PLIP interactions:20 interactions with chain C, 4 interactions with chain A- Hydrophobic interactions: C:F.448, C:F.448, C:F.452, C:L.477, C:I.480, A:V.26, A:V.52, A:T.76
- Hydrogen bonds: C:L.396, C:S.397, C:S.397, C:G.420, C:L.422, C:G.446, C:F.448, C:D.449, C:N.474, C:Y.476, C:G.478, C:L.479, A:Q.116
- Water bridges: C:S.397, C:D.447, C:N.474
TPP.20: 26 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, 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
20 PLIP interactions:17 interactions with chain D, 3 interactions with chain B- Hydrophobic interactions: D:F.452, D:L.477, D:L.477, B:V.26, B:T.76
- Hydrogen bonds: D:L.396, D:S.397, D:G.420, D:L.422, D:G.446, D:F.448, D:D.449, D:N.474, D:G.478, D:L.479, B:Q.116
- Water bridges: D:S.397, D:D.447, D:D.447, D:D.449
- 6 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.7
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.20
MG.10: 6 residues within 4Å:- Chain B: F.452, L.453, E.455
- Chain D: F.452, L.453, E.455
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.16: 4 residues within 4Å:- Chain C: D.447, N.474, Y.476
- Ligands: TPP.15
3 PLIP interactions:2 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:D.447, C:Y.476, H2O.36
MG.17: 6 residues within 4Å:- Chain A: F.452, L.453, E.455
- Chain C: F.452, L.453, E.455
4 PLIP interactions:2 interactions with chain C, 2 interactions with chain A- Metal complexes: C:F.452, C:E.455, A:F.452, A: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.53
- 8 x UQ0: 2,3-DIMETHOXY-5-METHYL-1,4-BENZOQUINONE(Covalent)(Non-covalent)
UQ0.4: 2 residues within 4Å:- Chain A: Q.354, C.589
No protein-ligand interaction detected (PLIP)UQ0.5: 5 residues within 4Å:- Chain A: H.46, L.48, F.463
- Chain C: Y.491, C.492
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:H.46, A:L.48, A:F.463
- Water bridges: A:Q.462
UQ0.6: 6 residues within 4Å:- Chain A: C.492, V.493, Q.494
- Chain C: H.46, L.48, F.463
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:H.46, C:L.48, C:Q.462
- pi-Stacking: C:F.463
UQ0.11: 4 residues within 4Å:- Chain B: E.250, 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: H.46, L.48, Q.462, F.463
- Chain D: C.492, Q.494
4 PLIP interactions:3 interactions with chain B, 1 interactions with chain D- Hydrophobic interactions: B:L.48, B:F.463
- Hydrogen bonds: B:Q.462
- Water bridges: D:C.492
UQ0.13: 7 residues within 4Å:- Chain B: C.492, V.493, Q.494
- Chain D: H.46, L.48, Q.462, F.463
4 PLIP interactions:3 interactions with chain B, 1 interactions with chain D- Hydrogen bonds: B:C.492, B:V.493, B:Q.494
- Hydrophobic interactions: D:F.463
UQ0.18: 3 residues within 4Å:- Chain C: E.250, Q.354, C.589
No protein-ligand interaction detected (PLIP)UQ0.22: 3 residues within 4Å:- Chain D: Q.354, R.358, C.589
2 PLIP interactions:2 interactions with chain D- Hydrophobic interactions: D:R.358
- Hydrogen bonds: D:R.358
- 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
CB
DC
ED
F
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.15 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)
- 4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)
- 6 x MG: MAGNESIUM ION(Non-covalent)
- 8 x UQ0: 2,3-DIMETHOXY-5-METHYL-1,4-BENZOQUINONE(Covalent)(Non-covalent)
- 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
CB
DC
ED
F