- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.85 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x MG: MAGNESIUM ION(Non-covalent)
- 4 x CL: CHLORIDE ION(Non-functional Binders)
CL.2: 6 residues within 4Å:- Chain A: C.230, V.231, T.256, A.298, I.299, Y.420
Ligand excluded by PLIPCL.7: 7 residues within 4Å:- Chain B: C.230, V.231, T.256, M.258, A.298, I.299, Y.420
Ligand excluded by PLIPCL.12: 6 residues within 4Å:- Chain C: C.230, V.231, T.256, A.298, I.299, Y.420
Ligand excluded by PLIPCL.17: 7 residues within 4Å:- Chain D: C.230, V.231, T.256, M.258, A.298, I.299, Y.420
Ligand excluded by PLIP- 4 x S1T: 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1S)-1-HYDROXYETHYL]-3-METHYL-2-THIENYL}ETHYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)
S1T.3: 24 residues within 4Å:- Chain A: M.400, G.401, D.402, A.422, G.423, M.424, G.448, D.449, G.450, A.451, N.476, S.478, W.479, E.480, M.481, L.482
- Chain B: P.43, G.44, D.45, E.68, T.91, A.94
- Ligands: MG.1, R1T.4
18 PLIP interactions:14 interactions with chain A, 4 interactions with chain B- Hydrophobic interactions: A:W.479, A:L.482, B:D.45, B:A.94
- Hydrogen bonds: A:D.402, A:A.422, A:M.424, A:G.450, A:A.451, A:N.476, A:E.480, A:M.481
- Water bridges: A:C.403, A:G.448, A:D.449, A:D.449, B:D.45, B:G.95
S1T.8: 25 residues within 4Å:- Chain A: P.43, G.44, D.45, E.68, T.91, G.95
- Chain B: M.400, G.401, D.402, A.422, G.423, M.424, G.448, D.449, G.450, A.451, M.454, N.476, S.478, W.479, E.480, M.481, L.482
- Ligands: MG.6, R1T.9
18 PLIP interactions:16 interactions with chain B, 2 interactions with chain A- Hydrophobic interactions: B:W.479, B:L.482, B:L.482, A:D.45
- Hydrogen bonds: B:D.402, B:A.422, B:A.422, B:M.424, B:G.448, B:G.450, B:A.451, B:N.476, B:E.480, B:M.481
- Water bridges: B:C.403, B:D.449, B:N.476, A:E.68
S1T.13: 24 residues within 4Å:- Chain C: M.400, G.401, D.402, A.422, G.423, M.424, G.448, D.449, G.450, A.451, N.476, S.478, W.479, E.480, M.481, L.482
- Chain D: P.43, G.44, D.45, E.68, T.91, A.94
- Ligands: MG.11, R1T.14
18 PLIP interactions:4 interactions with chain D, 14 interactions with chain C- Hydrophobic interactions: D:D.45, D:A.94, C:W.479, C:L.482
- Water bridges: D:D.45, D:G.95, C:C.403, C:G.448, C:D.449, C:D.449
- Hydrogen bonds: C:D.402, C:A.422, C:M.424, C:G.450, C:A.451, C:N.476, C:E.480, C:M.481
S1T.18: 25 residues within 4Å:- Chain C: P.43, G.44, D.45, E.68, T.91, G.95
- Chain D: M.400, G.401, D.402, A.422, G.423, M.424, G.448, D.449, G.450, A.451, M.454, N.476, S.478, W.479, E.480, M.481, L.482
- Ligands: MG.16, R1T.19
17 PLIP interactions:16 interactions with chain D, 1 interactions with chain C- Hydrophobic interactions: D:W.479, D:L.482, D:L.482, C:D.45
- Hydrogen bonds: D:D.402, D:A.422, D:A.422, D:M.424, D:G.448, D:G.450, D:A.451, D:N.476, D:E.480, D:M.481
- Water bridges: D:C.403, D:D.449, D:N.476
- 4 x R1T: 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1R)-1-HYDROXYETHYL]-3-METHYL-2-THIENYL}ETHYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)
R1T.4: 22 residues within 4Å:- Chain A: M.400, G.401, D.402, A.422, G.423, M.424, G.448, D.449, G.450, A.451, M.454, N.476, S.478, W.479, E.480, M.481, L.482
- Chain B: P.43, G.44, E.68
- Ligands: MG.1, S1T.3
18 PLIP interactions:16 interactions with chain A, 2 interactions with chain B- Hydrophobic interactions: A:W.479, A:L.482, A:L.482, A:L.482
- Hydrogen bonds: A:D.402, A:A.422, A:M.424, A:G.450, A:A.451, A:N.476, A:E.480, A:M.481
- Water bridges: A:C.403, A:G.448, A:D.449, A:D.449, B:D.45, B:G.95
R1T.9: 24 residues within 4Å:- Chain A: P.43, G.44, D.45, E.68, T.91, G.95
- Chain B: G.401, D.402, A.422, G.423, M.424, G.448, D.449, G.450, A.451, M.454, N.476, S.478, W.479, E.480, M.481, L.482
- Ligands: MG.6, S1T.8
18 PLIP interactions:16 interactions with chain B, 2 interactions with chain A- Hydrophobic interactions: B:M.424, B:W.479, B:L.482, B:L.482, A:T.91
- Hydrogen bonds: B:D.402, B:A.422, B:A.422, B:M.424, B:G.450, B:A.451, B:N.476, B:E.480, B:M.481
- Water bridges: B:C.403, B:D.449, B:N.476, A:D.45
R1T.14: 22 residues within 4Å:- Chain C: M.400, G.401, D.402, A.422, G.423, M.424, G.448, D.449, G.450, A.451, M.454, N.476, S.478, W.479, E.480, M.481, L.482
- Chain D: P.43, G.44, E.68
- Ligands: MG.11, S1T.13
18 PLIP interactions:2 interactions with chain D, 16 interactions with chain C- Water bridges: D:D.45, D:G.95, C:C.403, C:G.448, C:D.449, C:D.449
- Hydrophobic interactions: C:W.479, C:L.482, C:L.482, C:L.482
- Hydrogen bonds: C:D.402, C:A.422, C:M.424, C:G.450, C:A.451, C:N.476, C:E.480, C:M.481
R1T.19: 24 residues within 4Å:- Chain C: P.43, G.44, D.45, E.68, T.91, G.95
- Chain D: G.401, D.402, A.422, G.423, M.424, G.448, D.449, G.450, A.451, M.454, N.476, S.478, W.479, E.480, M.481, L.482
- Ligands: MG.16, S1T.18
18 PLIP interactions:16 interactions with chain D, 2 interactions with chain C- Hydrophobic interactions: D:M.424, D:W.479, D:L.482, D:L.482, C:T.91
- Hydrogen bonds: D:D.402, D:A.422, D:A.422, D:M.424, D:G.450, D:A.451, D:N.476, D:E.480, D:M.481
- Water bridges: D:C.403, D:D.449, D:N.476, C:D.45
- 4 x GOL: GLYCEROL(Non-functional Binders)
GOL.5: 7 residues within 4Å:- Chain A: S.83, T.84, P.112, R.173, S.176, R.235, Y.236
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:S.176
- Water bridges: A:S.83, A:T.84, A:L.85, A:Y.236
GOL.10: 7 residues within 4Å:- Chain B: S.83, T.84, P.112, R.173, S.176, R.235, Y.236
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:S.83, B:S.176
GOL.15: 7 residues within 4Å:- Chain C: S.83, T.84, P.112, R.173, S.176, R.235, Y.236
5 PLIP interactions:5 interactions with chain C- Hydrogen bonds: C:S.176
- Water bridges: C:S.83, C:T.84, C:L.85, C:Y.236
GOL.20: 7 residues within 4Å:- Chain D: S.83, T.84, P.112, R.173, S.176, R.235, Y.236
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:S.83, D:S.176
- Water bridges: D:T.84, D:T.84
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Versees, W. et al., Molecular mechanism of allosteric substrate activation in a thiamine diphosphate-dependent decarboxylase. J.Biol.Chem. (2007)
- Release Date
- 2007-10-23
- Peptides
- PHENYLPYRUVATE DECARBOXYLASE: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.85 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x MG: MAGNESIUM ION(Non-covalent)
- 4 x CL: CHLORIDE ION(Non-functional Binders)
- 4 x S1T: 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1S)-1-HYDROXYETHYL]-3-METHYL-2-THIENYL}ETHYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)
- 4 x R1T: 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1R)-1-HYDROXYETHYL]-3-METHYL-2-THIENYL}ETHYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)
- 4 x GOL: GLYCEROL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Versees, W. et al., Molecular mechanism of allosteric substrate activation in a thiamine diphosphate-dependent decarboxylase. J.Biol.Chem. (2007)
- Release Date
- 2007-10-23
- Peptides
- PHENYLPYRUVATE DECARBOXYLASE: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
B