- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.39 Å
- Oligo State
- homo-tetramer
- Ligands
- 8 x CA: CALCIUM ION(Non-covalent)
- 4 x NA: SODIUM ION(Non-functional Binders)
NA.3: 7 residues within 4Å:- Chain A: N.117, L.118, R.120
- Chain B: N.117, L.118, R.120
- Ligands: NA.9
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:N.117
NA.9: 7 residues within 4Å:- Chain A: N.117, L.118, R.120
- Chain B: N.117, L.118, R.120
- Ligands: NA.3
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:N.117
NA.15: 7 residues within 4Å:- Chain C: N.117, L.118, R.120
- Chain D: N.117, L.118, R.120
- Ligands: NA.21
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:L.118
NA.21: 7 residues within 4Å:- Chain C: N.117, L.118, R.120
- Chain D: N.117, L.118, R.120
- Ligands: NA.15
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:R.120
- 8 x GOL: GLYCEROL(Non-functional Binders)
GOL.4: 4 residues within 4Å:- Chain A: A.196, R.294, I.296, D.312
6 PLIP interactions:2 interactions with chain C, 4 interactions with chain A- Hydrogen bonds: C:H.178, A:R.294, A:R.294, A:D.312
- Water bridges: C:H.178, A:D.312
GOL.6: 6 residues within 4Å:- Chain A: L.43, Q.443, Y.444
- Chain B: G.475, L.476, D.477
4 PLIP interactions:3 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:G.475, B:D.477
- Water bridges: B:D.477, A:Q.443
GOL.10: 4 residues within 4Å:- Chain B: A.196, R.294, I.296, D.312
6 PLIP interactions:4 interactions with chain B, 2 interactions with chain D- Hydrogen bonds: B:R.294, B:R.294, B:D.312, D:H.178
- Water bridges: B:D.312, D:H.178
GOL.12: 6 residues within 4Å:- Chain A: G.475, L.476, D.477
- Chain B: L.43, Q.443, Y.444
4 PLIP interactions:3 interactions with chain A, 1 interactions with chain B- Hydrogen bonds: A:G.475, A:D.477
- Water bridges: A:D.477, B:Q.443
GOL.16: 4 residues within 4Å:- Chain C: A.196, R.294, I.296, D.312
4 PLIP interactions:1 interactions with chain A, 3 interactions with chain C- Hydrogen bonds: A:H.178, C:R.294, C:R.294
- Water bridges: C:D.312
GOL.18: 6 residues within 4Å:- Chain C: L.43, Q.443, Y.444
- Chain D: G.475, L.476, D.477
3 PLIP interactions:2 interactions with chain D, 1 interactions with chain C- Hydrogen bonds: D:G.475, D:D.477
- Water bridges: C:Q.443
GOL.22: 4 residues within 4Å:- Chain D: A.196, R.294, I.296, D.312
4 PLIP interactions:1 interactions with chain B, 3 interactions with chain D- Hydrogen bonds: B:H.178, D:R.294, D:R.294
- Water bridges: D:D.312
GOL.24: 6 residues within 4Å:- Chain C: G.475, L.476, D.477
- Chain D: L.43, Q.443, Y.444
3 PLIP interactions:2 interactions with chain C, 1 interactions with chain D- Hydrogen bonds: C:G.475, C:D.477
- Water bridges: D:Q.443
- 4 x TZD: 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)
TZD.5: 27 residues within 4Å:- Chain A: E.375, S.376, T.377, S.378, G.401, G.402, M.403, G.427, D.428, G.429, S.430, Y.433, N.455, T.457, Y.458, G.459, A.460, L.461
- Chain B: N.23, P.24, G.25, E.47, H.70, A.73, G.74, N.77
- Ligands: CA.1
17 PLIP interactions:16 interactions with chain A, 1 interactions with chain B- Hydrophobic interactions: A:Y.433, A:L.461
- Hydrogen bonds: A:T.377, A:S.378, A:G.401, A:M.403, A:G.427, A:G.429, A:S.430, A:S.430, A:Y.433, A:N.455, A:G.459, A:A.460
- Water bridges: A:D.428, A:N.455, B:H.70
TZD.11: 27 residues within 4Å:- Chain A: N.23, P.24, G.25, E.47, H.70, A.73, G.74, N.77
- Chain B: E.375, S.376, T.377, S.378, G.401, G.402, M.403, G.427, D.428, G.429, S.430, Y.433, N.455, T.457, Y.458, G.459, A.460, L.461
- Ligands: CA.7
17 PLIP interactions:16 interactions with chain B, 1 interactions with chain A- Hydrophobic interactions: B:Y.433, B:L.461
- Hydrogen bonds: B:T.377, B:S.378, B:G.401, B:M.403, B:G.427, B:G.429, B:S.430, B:S.430, B:Y.433, B:N.455, B:G.459, B:A.460
- Water bridges: B:D.428, B:N.455, A:H.70
TZD.17: 27 residues within 4Å:- Chain C: E.375, S.376, T.377, S.378, G.401, G.402, M.403, G.427, D.428, G.429, S.430, Y.433, N.455, T.457, Y.458, G.459, A.460, L.461
- Chain D: N.23, P.24, G.25, E.47, H.70, A.73, G.74, N.77
- Ligands: CA.13
18 PLIP interactions:17 interactions with chain C, 1 interactions with chain D- Hydrophobic interactions: C:Y.433, C:L.461
- Hydrogen bonds: C:T.377, C:T.377, C:S.378, C:G.401, C:M.403, C:G.427, C:G.429, C:S.430, C:S.430, C:N.455, C:N.455, C:G.459, C:A.460
- Water bridges: C:D.428, C:N.455, D:H.70
TZD.23: 27 residues within 4Å:- Chain C: N.23, P.24, G.25, E.47, H.70, A.73, G.74, N.77
- Chain D: E.375, S.376, T.377, S.378, G.401, G.402, M.403, G.427, D.428, G.429, S.430, Y.433, N.455, T.457, Y.458, G.459, A.460, L.461
- Ligands: CA.19
17 PLIP interactions:16 interactions with chain D, 1 interactions with chain C- Hydrophobic interactions: D:Y.433, D:L.461
- Hydrogen bonds: D:T.377, D:T.377, D:S.378, D:G.401, D:M.403, D:G.427, D:G.429, D:S.430, D:S.430, D:N.455, D:G.459, D:A.460
- Water bridges: D:D.428, D:N.455, C:H.70
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Andrews, F.H. et al., A bulky hydrophobic residue is not required to maintain the v-conformation of enzyme-bound thiamin diphosphate. Biochemistry (2013)
- Release Date
- 2013-05-22
- Peptides
- Benzoylformate decarboxylase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.39 Å
- Oligo State
- homo-tetramer
- Ligands
- 8 x CA: CALCIUM ION(Non-covalent)
- 4 x NA: SODIUM ION(Non-functional Binders)
- 8 x GOL: GLYCEROL(Non-functional Binders)
- 4 x TZD: 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Andrews, F.H. et al., A bulky hydrophobic residue is not required to maintain the v-conformation of enzyme-bound thiamin diphosphate. Biochemistry (2013)
- Release Date
- 2013-05-22
- Peptides
- Benzoylformate decarboxylase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
A