- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.15 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x MG: MAGNESIUM ION(Non-covalent)
- 4 x TPW: 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)
TPW.2: 23 residues within 4Å:- Chain A: 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, A.94, H.133
- Ligands: MG.1, PPY.7
17 PLIP interactions:17 interactions with chain A- Hydrophobic interactions: A:W.479, A:W.479, A:L.482
- Hydrogen bonds: A:M.400, 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:G.448, A:D.449, A:N.476
TPW.6: 24 residues within 4Å:- Chain A: I.42, P.43, G.44, E.68, A.94, H.133
- 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: PPY.3, MG.5
17 PLIP interactions:16 interactions with chain B, 1 interactions with chain A- Hydrophobic interactions: B:W.479, B:W.479, B:L.482, B:L.482, B:L.482, A:A.94
- Hydrogen bonds: B:D.402, 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
TPW.11: 23 residues within 4Å:- Chain C: 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, A.94, H.133
- Ligands: MG.10, PPY.16
18 PLIP interactions:17 interactions with chain C, 1 interactions with chain D- Hydrophobic interactions: C:W.479, C:W.479, C:L.482
- Hydrogen bonds: C:M.400, C:D.402, C:A.422, C:M.424, C:G.450, C:A.451, C:N.476, C:E.480, C:M.481
- Water bridges: C:C.403, C:G.448, C:G.448, C:D.449, C:N.476, D:E.68
TPW.15: 24 residues within 4Å:- Chain C: I.42, P.43, G.44, E.68, A.94, H.133
- 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: PPY.12, MG.14
18 PLIP interactions:16 interactions with chain D, 2 interactions with chain C- Hydrophobic interactions: D:W.479, D:W.479, D:L.482, D:L.482, D:L.482, C:A.94
- Hydrogen bonds: D:D.402, 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:E.68
- 8 x PPY: 3-PHENYLPYRUVIC ACID(Non-covalent)
PPY.3: 12 residues within 4Å:- Chain A: G.44, D.45, H.132, H.133
- Chain B: T.303, A.422, M.481, L.482, F.485, F.552, Q.556
- Ligands: TPW.6
10 PLIP interactions:5 interactions with chain A, 5 interactions with chain B- Hydrogen bonds: A:D.45, A:D.45
- Water bridges: A:F.46
- Salt bridges: A:H.133
- pi-Stacking: A:H.132
- Hydrophobic interactions: B:T.303, B:A.422, B:F.485, B:F.552, B:Q.556
PPY.4: 12 residues within 4Å:- Chain A: R.80, R.234, R.235, M.258, R.260, G.261, L.262, L.395, G.414, L.415, M.416, A.417
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:L.262, A:L.395
- Hydrogen bonds: A:A.417
- Salt bridges: A:R.80, A:R.235
PPY.7: 12 residues within 4Å:- Chain A: T.303, A.422, M.481, L.482, F.485, F.552, Q.556
- Chain B: G.44, D.45, H.132, H.133
- Ligands: TPW.2
8 PLIP interactions:5 interactions with chain B, 3 interactions with chain A- Hydrogen bonds: B:D.45, B:D.45
- Water bridges: B:F.46
- Salt bridges: B:H.133
- pi-Stacking: B:H.132
- Hydrophobic interactions: A:T.303, A:F.485, A:F.552
PPY.8: 11 residues within 4Å:- Chain B: R.80, R.234, R.235, M.258, R.260, G.261, L.262, G.414, L.415, M.416, A.417
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:A.417
- Salt bridges: B:R.80, B:R.235
PPY.12: 12 residues within 4Å:- Chain C: G.44, D.45, H.132, H.133
- Chain D: T.303, A.422, M.481, L.482, F.485, F.552, Q.556
- Ligands: TPW.15
9 PLIP interactions:5 interactions with chain D, 4 interactions with chain C- Hydrophobic interactions: D:T.303, D:A.422, D:F.485, D:F.552, D:Q.556
- Hydrogen bonds: C:D.45
- Water bridges: C:F.46
- Salt bridges: C:H.133
- pi-Stacking: C:H.132
PPY.13: 12 residues within 4Å:- Chain C: R.80, R.234, R.235, M.258, R.260, G.261, L.262, L.395, G.414, L.415, M.416, A.417
5 PLIP interactions:5 interactions with chain C- Hydrophobic interactions: C:L.262, C:L.395
- Hydrogen bonds: C:A.417
- Salt bridges: C:R.80, C:R.235
PPY.16: 12 residues within 4Å:- Chain C: T.303, A.422, M.481, L.482, F.485, F.552, Q.556
- Chain D: G.44, D.45, H.132, H.133
- Ligands: TPW.11
7 PLIP interactions:4 interactions with chain D, 3 interactions with chain C- Hydrogen bonds: D:D.45
- Water bridges: D:F.46
- Salt bridges: D:H.133
- pi-Stacking: D:H.132
- Hydrophobic interactions: C:T.303, C:F.485, C:F.552
PPY.17: 11 residues within 4Å:- Chain D: R.80, R.234, R.235, M.258, R.260, G.261, L.262, G.414, L.415, M.416, A.417
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:A.417
- Salt bridges: D:R.80, D:R.235
- 2 x GOL: GLYCEROL(Non-functional Binders)
GOL.9: 3 residues within 4Å:- Chain B: V.544, L.545, D.547
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:L.545
- Water bridges: B:D.547, B:D.547
GOL.18: 3 residues within 4Å:- Chain D: V.544, L.545, D.547
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:L.545
- Water bridges: D:D.547
- 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 2.15 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x MG: MAGNESIUM ION(Non-covalent)
- 4 x TPW: 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)
- 8 x PPY: 3-PHENYLPYRUVIC ACID(Non-covalent)
- 2 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