- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.07 Å
- Oligo State
- homo-tetramer
- Ligands
- 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)
- 8 x CA: CALCIUM ION(Non-covalent)
CA.2: 4 residues within 4Å:- Chain A: D.428, N.455, T.457
- Ligands: TZD.1
3 PLIP interactions:2 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.428, A:T.457, H2O.1
CA.3: 1 residues within 4Å:- Chain A: D.364
5 PLIP interactions:1 interactions with chain A, 4 Ligand-Water interactions- Metal complexes: A:D.364, H2O.3, H2O.13, H2O.13, H2O.22
CA.8: 4 residues within 4Å:- Chain B: D.428, N.455, T.457
- Ligands: TZD.7
3 PLIP interactions:2 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:D.428, B:T.457, H2O.23
CA.9: 1 residues within 4Å:- Chain B: D.364
5 PLIP interactions:1 interactions with chain B, 4 Ligand-Water interactions- Metal complexes: B:D.364, H2O.25, H2O.35, H2O.35, H2O.44
CA.14: 4 residues within 4Å:- Chain C: D.428, N.455, T.457
- Ligands: TZD.13
3 PLIP interactions:2 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:D.428, C:T.457, H2O.45
CA.15: 1 residues within 4Å:- Chain C: D.364
5 PLIP interactions:1 interactions with chain C, 4 Ligand-Water interactions- Metal complexes: C:D.364, H2O.47, H2O.57, H2O.57, H2O.66
CA.20: 4 residues within 4Å:- Chain D: D.428, N.455, T.457
- Ligands: TZD.19
3 PLIP interactions:2 interactions with chain D, 1 Ligand-Water interactions- Metal complexes: D:D.428, D:T.457, H2O.67
CA.21: 1 residues within 4Å:- Chain D: D.364
5 PLIP interactions:1 interactions with chain D, 4 Ligand-Water interactions- Metal complexes: D:D.364, H2O.69, H2O.79, H2O.79, H2O.88
- 4 x NA: SODIUM ION(Non-functional Binders)
NA.4: 7 residues within 4Å:- Chain A: N.117, L.118, R.120
- Chain B: N.117, L.118, R.120
- Ligands: NA.10
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:N.117
NA.10: 7 residues within 4Å:- Chain A: N.117, L.118, R.120
- Chain B: N.117, L.118, R.120
- Ligands: NA.4
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:R.120
NA.16: 7 residues within 4Å:- Chain C: N.117, L.118, R.120
- Chain D: N.117, L.118, R.120
- Ligands: NA.22
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:R.120
NA.22: 7 residues within 4Å:- Chain C: N.117, L.118, R.120
- Chain D: N.117, L.118, R.120
- Ligands: NA.16
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:N.117
- 8 x GOL: GLYCEROL(Non-functional Binders)
GOL.5: 6 residues within 4Å:- Chain A: L.43, Q.443, Y.444
- Chain B: G.475, L.476, D.477
5 PLIP interactions:4 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:G.475, B:D.477
- Water bridges: B:L.476, B:D.477, A:Q.443
GOL.6: 5 residues within 4Å:- Chain A: A.196, R.294, I.296, D.312
- Chain C: H.178
6 PLIP interactions:4 interactions with chain A, 2 interactions with chain C- Hydrogen bonds: A:R.294, A:R.294, A:D.312, C:H.178
- Water bridges: A:D.312, C:H.178
GOL.11: 6 residues within 4Å:- Chain A: G.475, L.476, D.477
- Chain B: L.43, Q.443, Y.444
5 PLIP interactions:1 interactions with chain B, 4 interactions with chain A- Water bridges: B:Q.443, A:L.476, A:D.477
- Hydrogen bonds: A:G.475, A:D.477
GOL.12: 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.17: 6 residues within 4Å:- Chain C: L.43, Q.443, Y.444
- Chain D: G.475, L.476, D.477
5 PLIP interactions:4 interactions with chain D, 1 interactions with chain C- Hydrogen bonds: D:G.475, D:D.477
- Water bridges: D:L.476, D:D.477, C:Q.443
GOL.18: 5 residues within 4Å:- Chain A: H.178
- 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.23: 6 residues within 4Å:- Chain C: G.475, L.476, D.477
- Chain D: L.43, Q.443, Y.444
5 PLIP interactions:4 interactions with chain C, 1 interactions with chain D- Hydrogen bonds: C:G.475, C:D.477
- Water bridges: C:L.476, C:D.477, D:Q.443
GOL.24: 5 residues within 4Å:- Chain B: H.178
- 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
- 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 1.07 Å
- Oligo State
- homo-tetramer
- Ligands
- 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)
- 8 x CA: CALCIUM ION(Non-covalent)
- 4 x NA: SODIUM ION(Non-functional Binders)
- 8 x GOL: GLYCEROL(Non-functional Binders)
- 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