- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.43 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)
- 4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)
TPP.2: 27 residues within 4Å:- Chain A: I.398, G.399, N.400, H.401, G.424, I.425, L.426, G.450, D.451, G.452, A.453, Y.456, N.478, S.480, Y.481, G.482, A.483, N.484
- Chain B: F.25, I.26, G.27, E.52, H.76, V.78, G.79
- Ligands: MG.5, CL.17
22 PLIP interactions:2 interactions with chain B, 20 interactions with chain A- Hydrophobic interactions: B:F.25, A:I.425, A:L.426, A:L.426, A:Y.481, A:Y.481
- Water bridges: B:E.52, A:N.478, A:N.478
- Hydrogen bonds: A:N.400, A:H.401, A:G.424, A:L.426, A:D.451, A:G.452, A:A.453, A:Y.456, A:N.478, A:G.482, A:A.483
- Salt bridges: A:H.401, A:H.401
TPP.15: 26 residues within 4Å:- Chain A: F.25, I.26, G.27, E.52, H.76, V.78, G.79
- Chain B: I.398, G.399, N.400, H.401, G.424, L.426, G.450, D.451, G.452, A.453, Y.456, N.478, S.480, Y.481, G.482, A.483, N.484
- Ligands: CL.4, MG.19
19 PLIP interactions:17 interactions with chain B, 2 interactions with chain A- Hydrophobic interactions: B:L.426, B:L.426, B:Y.481, B:Y.481, A:F.25
- Hydrogen bonds: B:N.400, B:H.401, B:G.424, B:L.426, B:D.451, B:D.451, B:G.452, B:A.453, B:N.478, B:G.482, B:A.483
- Salt bridges: B:H.401, B:H.401
- Water bridges: A:G.79
TPP.29: 27 residues within 4Å:- Chain C: I.398, G.399, N.400, H.401, G.424, I.425, L.426, G.450, D.451, G.452, A.453, Y.456, N.478, S.480, Y.481, G.482, A.483, N.484
- Chain D: F.25, I.26, G.27, E.52, H.76, V.78, G.79
- Ligands: MG.32, CL.44
21 PLIP interactions:19 interactions with chain C, 2 interactions with chain D- Hydrophobic interactions: C:I.425, C:L.426, C:L.426, C:Y.481, C:Y.481, D:F.25
- Hydrogen bonds: C:N.400, C:H.401, C:G.424, C:L.426, C:D.451, C:G.452, C:A.453, C:N.478, C:G.482, C:A.483
- Water bridges: C:N.478, C:N.478, D:G.79
- Salt bridges: C:H.401, C:H.401
TPP.42: 26 residues within 4Å:- Chain C: F.25, I.26, G.27, E.52, H.76, V.78, G.79
- Chain D: I.398, G.399, N.400, H.401, G.424, L.426, G.450, D.451, G.452, A.453, Y.456, N.478, S.480, Y.481, G.482, A.483, N.484
- Ligands: CL.31, MG.46
19 PLIP interactions:17 interactions with chain D, 2 interactions with chain C- Hydrophobic interactions: D:L.426, D:L.426, D:Y.481, D:Y.481, C:F.25
- Hydrogen bonds: D:N.400, D:H.401, D:G.424, D:L.426, D:D.451, D:G.452, D:A.453, D:Y.456, D:N.478, D:G.482, D:A.483
- Salt bridges: D:H.401, D:H.401
- Water bridges: C:E.52
- 4 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)
MES.3: 11 residues within 4Å:- Chain A: L.202, V.203, A.204, A.205, K.206, P.208, V.232, G.233, R.347, E.348, N.349
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:E.348
MES.16: 6 residues within 4Å:- Chain B: Q.494, N.495, N.496, W.497, T.498, E.499
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:N.495, B:W.497, B:T.498, B:E.499
MES.30: 11 residues within 4Å:- Chain C: L.202, V.203, A.204, A.205, K.206, P.208, V.232, G.233, R.347, E.348, N.349
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:E.348
MES.43: 6 residues within 4Å:- Chain D: Q.494, N.495, N.496, W.497, T.498, E.499
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:N.495, D:W.497, D:T.498, D:E.499
- 4 x CL: CHLORIDE ION(Non-functional Binders)
CL.4: 5 residues within 4Å:- Chain A: H.28, H.76, Q.116
- Chain B: W.285
- Ligands: TPP.15
Ligand excluded by PLIPCL.17: 5 residues within 4Å:- Chain A: W.285
- Chain B: H.28, H.76, Q.116
- Ligands: TPP.2
Ligand excluded by PLIPCL.31: 5 residues within 4Å:- Chain C: H.28, H.76, Q.116
- Chain D: W.285
- Ligands: TPP.42
Ligand excluded by PLIPCL.44: 5 residues within 4Å:- Chain C: W.285
- Chain D: H.28, H.76, Q.116
- Ligands: TPP.29
Ligand excluded by PLIP- 6 x MG: MAGNESIUM ION(Non-covalent)
MG.5: 4 residues within 4Å:- Chain A: D.451, N.478, S.480
- Ligands: TPP.2
3 PLIP interactions:2 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.451, A:S.480, H2O.16
MG.18: 5 residues within 4Å:- Chain B: R.148, R.183, A.184
- Chain D: L.308
- Ligands: PG4.27
No protein-ligand interaction detected (PLIP)MG.19: 4 residues within 4Å:- Chain B: D.451, N.478, S.480
- Ligands: TPP.15
3 PLIP interactions:2 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:D.451, B:S.480, H2O.34
MG.32: 4 residues within 4Å:- Chain C: D.451, N.478, S.480
- Ligands: TPP.29
3 PLIP interactions:2 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:D.451, C:S.480, H2O.54
MG.45: 5 residues within 4Å:- Chain B: L.308
- Chain D: R.148, R.183, A.184
- Ligands: PG4.54
No protein-ligand interaction detected (PLIP)MG.46: 4 residues within 4Å:- Chain D: D.451, N.478, S.480
- Ligands: TPP.42
3 PLIP interactions:2 interactions with chain D, 1 Ligand-Water interactions- Metal complexes: D:D.451, D:S.480, H2O.71
- 4 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)
P6G.6: 4 residues within 4Å:- Chain A: P.374, A.375, S.376
- Ligands: P6G.8
1 PLIP interactions:1 interactions with chain A- Water bridges: A:S.546
P6G.8: 3 residues within 4Å:- Chain A: T.548, S.553
- Ligands: P6G.6
3 PLIP interactions:3 interactions with chain A- Water bridges: A:T.548, A:T.548, A:S.553
P6G.33: 4 residues within 4Å:- Chain C: P.374, A.375, S.376
- Ligands: P6G.35
1 PLIP interactions:1 interactions with chain C- Water bridges: C:S.546
P6G.35: 3 residues within 4Å:- Chain C: T.548, S.553
- Ligands: P6G.33
2 PLIP interactions:2 interactions with chain C- Water bridges: C:T.548, C:S.553
- 2 x 1PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL(Non-covalent)
1PG.7: 5 residues within 4Å:- Chain A: G.513, A.514, Y.515, S.535, K.537
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:K.537
- Hydrogen bonds: A:K.537
1PG.34: 5 residues within 4Å:- Chain C: G.513, A.514, Y.515, S.535, K.537
2 PLIP interactions:2 interactions with chain C- Hydrophobic interactions: C:K.537
- Hydrogen bonds: C:K.537
- 18 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)
PG4.9: 8 residues within 4Å:- Chain A: A.109, Q.117, V.118, P.119, W.120, R.132
- Chain D: E.134
- Ligands: PG4.26
Ligand excluded by PLIPPG4.12: 2 residues within 4Å:- Chain A: E.466, H.467
Ligand excluded by PLIPPG4.13: 3 residues within 4Å:- Chain A: E.15, E.16, H.41
Ligand excluded by PLIPPG4.21: 8 residues within 4Å:- Chain A: E.134, R.135
- Chain B: R.568
- Chain C: R.568, I.570, P.571
- Chain D: E.134, R.135
Ligand excluded by PLIPPG4.23: 3 residues within 4Å:- Chain B: G.338, F.339, K.340
Ligand excluded by PLIPPG4.24: 7 residues within 4Å:- Chain B: E.366, Q.367, S.369, P.374, A.375, S.376, Q.549
Ligand excluded by PLIPPG4.25: 7 residues within 4Å:- Chain B: A.109, Q.117, V.118, P.119, W.120, R.132
- Chain C: E.134
Ligand excluded by PLIPPG4.26: 7 residues within 4Å:- Chain B: R.91, T.124, P.125, A.127, R.128
- Ligands: PG4.9, PG4.53
Ligand excluded by PLIPPG4.27: 6 residues within 4Å:- Chain B: F.147, R.148, E.151, R.183
- Ligands: MG.18, 2PE.47
Ligand excluded by PLIPPG4.36: 8 residues within 4Å:- Chain B: E.134
- Chain C: A.109, Q.117, V.118, P.119, W.120, R.132
- Ligands: PG4.53
Ligand excluded by PLIPPG4.39: 2 residues within 4Å:- Chain C: E.466, H.467
Ligand excluded by PLIPPG4.40: 3 residues within 4Å:- Chain C: E.15, E.16, H.41
Ligand excluded by PLIPPG4.48: 8 residues within 4Å:- Chain A: R.568, I.570, P.571
- Chain B: E.134, R.135
- Chain C: E.134, R.135
- Chain D: R.568
Ligand excluded by PLIPPG4.50: 3 residues within 4Å:- Chain D: G.338, F.339, K.340
Ligand excluded by PLIPPG4.51: 7 residues within 4Å:- Chain D: E.366, Q.367, S.369, P.374, A.375, S.376, Q.549
Ligand excluded by PLIPPG4.52: 7 residues within 4Å:- Chain A: E.134
- Chain D: A.109, Q.117, V.118, P.119, W.120, R.132
Ligand excluded by PLIPPG4.53: 7 residues within 4Å:- Chain D: R.91, T.124, P.125, A.127, R.128
- Ligands: PG4.26, PG4.36
Ligand excluded by PLIPPG4.54: 6 residues within 4Å:- Chain D: F.147, R.148, E.151, R.183
- Ligands: 2PE.20, MG.45
Ligand excluded by PLIP- 2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
PEG.10: 6 residues within 4Å:- Chain A: R.91, T.124, P.125, A.127, R.128
- Ligands: PEG.37
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:R.91, A:R.91, A:P.125
PEG.37: 6 residues within 4Å:- Chain C: R.91, T.124, P.125, A.127, R.128
- Ligands: PEG.10
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:R.91, C:R.91, C:P.125
- 6 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)
2PE.11: 4 residues within 4Å:- Chain A: R.444, I.533, D.534, G.536
1 PLIP interactions:1 interactions with chain A- Water bridges: A:R.444
2PE.20: 18 residues within 4Å:- Chain B: E.151, H.153, A.184, K.185, S.186, L.188, T.303, P.305, V.319
- Chain D: H.153, R.183, A.184, K.185, L.188, T.303, P.305
- Ligands: 2PE.47, PG4.54
7 PLIP interactions:6 interactions with chain B, 1 interactions with chain D- Hydrogen bonds: B:H.153
- Water bridges: B:E.151, B:H.153, B:R.183, B:A.184, B:S.186, D:H.153
2PE.22: 10 residues within 4Å:- Chain B: K.386, V.387, Q.388, R.389, P.390, P.441, N.442, S.443, R.444, P.470
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:P.441, B:R.444, B:R.444
2PE.38: 4 residues within 4Å:- Chain C: R.444, I.533, D.534, G.536
1 PLIP interactions:1 interactions with chain C- Water bridges: C:R.444
2PE.47: 18 residues within 4Å:- Chain B: H.153, R.183, A.184, K.185, L.188, T.303, P.305
- Chain D: E.151, H.153, A.184, K.185, S.186, L.188, T.303, P.305, V.319
- Ligands: 2PE.20, PG4.27
7 PLIP interactions:5 interactions with chain D, 2 interactions with chain B- Water bridges: D:E.151, D:H.153, D:R.183, D:A.184, D:S.186, B:H.153, B:H.153
2PE.49: 10 residues within 4Å:- Chain D: K.386, V.387, Q.388, R.389, P.390, P.441, N.442, S.443, R.444, P.470
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:P.441, D:R.444, D:R.444
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Loschonsky, S. et al., Extended Reaction Scope of Thiamine Diphosphate Dependent Cyclohexane-1,2-Dione Hydrolase: From C-C Bond Cleavage to C-C Bond Ligation. Angew.Chem.Int.Ed.Engl. (2014)
- Release Date
- 2015-01-21
- Peptides
- CYCLOHEXANE-1,2-DIONE HYDROLASE: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.43 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)
- 4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)
- 4 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)
- 4 x CL: CHLORIDE ION(Non-functional Binders)
- 6 x MG: MAGNESIUM ION(Non-covalent)
- 4 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)
- 2 x 1PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL(Non-covalent)
- 18 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)
- 2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 6 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Loschonsky, S. et al., Extended Reaction Scope of Thiamine Diphosphate Dependent Cyclohexane-1,2-Dione Hydrolase: From C-C Bond Cleavage to C-C Bond Ligation. Angew.Chem.Int.Ed.Engl. (2014)
- Release Date
- 2015-01-21
- Peptides
- CYCLOHEXANE-1,2-DIONE HYDROLASE: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
B