- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.26 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 A- Hydrogen bonds: A: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 A- Hydrogen bonds: A:R.120
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:N.117
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:L.118
- 8 x GOL: GLYCEROL(Non-functional Binders)
GOL.4: 5 residues within 4Å:- Chain A: A.196, R.294, I.296, D.312
- Chain C: H.178
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.5: 6 residues within 4Å:- Chain A: L.43, Q.443, Y.444
- Chain B: G.475, L.476, D.477
6 PLIP interactions:2 interactions with chain A, 4 interactions with chain B- Water bridges: A:Q.443, A:Q.443, B:L.476, B:D.477
- Hydrogen bonds: B:G.475, B:D.477
GOL.10: 5 residues within 4Å:- Chain B: A.196, R.294, I.296, D.312
- Chain D: H.178
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.11: 6 residues within 4Å:- Chain A: G.475, L.476, D.477
- Chain B: L.43, Q.443, Y.444
6 PLIP interactions:4 interactions with chain A, 2 interactions with chain B- Hydrogen bonds: A:G.475, A:D.477
- Water bridges: A:L.476, A:D.477, B:Q.443, B:Q.443
GOL.16: 5 residues within 4Å:- Chain A: H.178
- Chain C: A.196, R.294, I.296, D.312
4 PLIP interactions:3 interactions with chain C, 1 interactions with chain A- Hydrogen bonds: C:R.294, C:R.294, A:H.178
- Water bridges: C:D.312
GOL.17: 6 residues within 4Å:- Chain C: L.43, Q.443, Y.444
- Chain D: G.475, L.476, D.477
6 PLIP interactions:2 interactions with chain C, 4 interactions with chain D- Water bridges: C:Q.443, C:Q.443, D:L.476, D:D.477
- Hydrogen bonds: D:G.475, D:D.477
GOL.22: 5 residues within 4Å:- Chain B: H.178
- Chain D: A.196, R.294, I.296, D.312
4 PLIP interactions:3 interactions with chain D, 1 interactions with chain B- Hydrogen bonds: D:R.294, D:R.294, B:H.178
- Water bridges: D:D.312
GOL.23: 6 residues within 4Å:- Chain C: G.475, L.476, D.477
- Chain D: L.43, Q.443, Y.444
6 PLIP interactions:4 interactions with chain C, 2 interactions with chain D- Hydrogen bonds: C:G.475, C:D.477
- Water bridges: C:L.476, C:D.477, D:Q.443, 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.6: 25 residues within 4Å:- Chain A: E.375, S.376, T.377, S.378, G.401, G.402, S.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, N.77
- Ligands: CA.1
17 PLIP interactions:17 interactions with chain A- Hydrophobic interactions: A:Y.433, A:L.461
- Hydrogen bonds: A:T.377, A:S.378, A:S.378, A:G.401, A:S.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
TZD.12: 25 residues within 4Å:- Chain A: N.23, P.24, G.25, E.47, H.70, N.77
- Chain B: E.375, S.376, T.377, S.378, G.401, G.402, S.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:17 interactions with chain B- Hydrophobic interactions: B:Y.433, B:L.461
- Hydrogen bonds: B:T.377, B:S.378, B:S.378, B:G.401, B:S.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
TZD.18: 25 residues within 4Å:- Chain C: E.375, S.376, T.377, S.378, G.401, G.402, S.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, N.77
- Ligands: CA.13
19 PLIP interactions:19 interactions with chain C- Hydrophobic interactions: C:Y.433, C:L.461
- Hydrogen bonds: C:T.377, C:T.377, C:S.378, C:S.378, C:G.401, C:S.403, C:G.427, C:D.428, 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
TZD.24: 25 residues within 4Å:- Chain C: N.23, P.24, G.25, E.47, H.70, N.77
- Chain D: E.375, S.376, T.377, S.378, G.401, G.402, S.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
18 PLIP interactions:18 interactions with chain D- Hydrophobic interactions: D:Y.433, D:L.461
- Hydrogen bonds: D:T.377, D:T.377, D:S.378, D:S.378, D:G.401, D:S.403, D:G.427, D:D.428, 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
- 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 1.26 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