- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.39 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)
- 4 x UMP: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE(Non-covalent)
UMP.2: 12 residues within 4Å:- Chain A: F.89, E.98, L.99, S.100, G.101, R.102, R.159
- Chain D: R.86, Q.87, R.90, R.186
- Ligands: FAD.1
20 PLIP interactions:12 interactions with chain D, 8 interactions with chain A- Hydrophobic interactions: D:R.90
- Hydrogen bonds: D:Q.87, D:R.90, D:R.186, D:R.186, A:E.98, A:G.101, A:R.102, A:R.102
- Water bridges: D:R.86, D:R.86, D:R.86, D:R.86, D:Q.87, D:Q.192, A:E.98, A:E.98, A:R.159
- Salt bridges: D:R.86, A:R.159
UMP.8: 12 residues within 4Å:- Chain B: F.89, E.98, L.99, S.100, G.101, R.102, R.159
- Chain C: R.86, Q.87, R.90, R.186
- Ligands: FAD.7
19 PLIP interactions:7 interactions with chain B, 12 interactions with chain C- Hydrogen bonds: B:G.101, B:R.102, B:R.102, C:Q.87, C:R.90, C:R.186, C:R.186
- Water bridges: B:E.98, B:E.98, B:R.159, C:R.86, C:R.86, C:R.86, C:R.86, C:Q.87, C:Q.192
- Salt bridges: B:R.159, C:R.86
- Hydrophobic interactions: C:R.90
UMP.14: 12 residues within 4Å:- Chain B: R.86, Q.87, R.90, R.186
- Chain C: F.89, E.98, L.99, S.100, G.101, R.102, R.159
- Ligands: FAD.13
20 PLIP interactions:12 interactions with chain B, 8 interactions with chain C- Hydrophobic interactions: B:R.90
- Hydrogen bonds: B:Q.87, B:R.90, B:R.186, B:R.186, C:E.98, C:G.101, C:R.102, C:R.102
- Water bridges: B:R.86, B:R.86, B:R.86, B:R.86, B:Q.87, B:Q.192, C:E.98, C:E.98, C:R.159
- Salt bridges: B:R.86, C:R.159
UMP.20: 12 residues within 4Å:- Chain A: R.86, Q.87, R.90, R.186
- Chain D: F.89, E.98, L.99, S.100, G.101, R.102, R.159
- Ligands: FAD.19
19 PLIP interactions:12 interactions with chain A, 7 interactions with chain D- Hydrophobic interactions: A:R.90
- Hydrogen bonds: A:Q.87, A:R.90, A:R.186, A:R.186, D:G.101, D:R.102, D:R.102
- Water bridges: A:R.86, A:R.86, A:R.86, A:R.86, A:Q.87, A:Q.192, D:E.98, D:E.98, D:R.159
- Salt bridges: A:R.86, D:R.159
- 8 x MEF: N-({4-[(6aR)-3-amino-1-oxo-1,2,5,6,6a,7-hexahydroimidazo[1,5-f]pteridin-8(9H)-yl]phenyl}carbonyl)-L-glutamic acid(Non-covalent)
MEF.3: 11 residues within 4Å:- Chain A: N.97
- Chain C: A.39, R.40, L.56, L.60, H.65, T.67, P.68
- Chain D: L.185
- Ligands: FAD.1, PEG.5
8 PLIP interactions:8 interactions with chain C- Hydrophobic interactions: C:A.39, C:L.56
- Hydrogen bonds: C:T.67
- Water bridges: C:H.65, C:H.65, C:E.66, C:T.67
- pi-Stacking: C:H.65
MEF.4: 8 residues within 4Å:- Chain A: L.118, Y.121, K.122, T.123, T.124, I.125, P.126, P.127
6 PLIP interactions:6 interactions with chain A- Hydrophobic interactions: A:P.126
- Hydrogen bonds: A:Y.121, A:Y.121, A:T.123, A:T.124
- Water bridges: A:G.120
MEF.9: 11 residues within 4Å:- Chain B: N.97
- Chain C: L.185
- Chain D: A.39, R.40, L.56, L.60, H.65, T.67, P.68
- Ligands: FAD.7, PEG.11
8 PLIP interactions:8 interactions with chain D- Hydrophobic interactions: D:A.39, D:L.56
- Hydrogen bonds: D:T.67
- Water bridges: D:H.65, D:H.65, D:E.66, D:T.67
- pi-Stacking: D:H.65
MEF.10: 8 residues within 4Å:- Chain B: L.118, Y.121, K.122, T.123, T.124, I.125, P.126, P.127
6 PLIP interactions:6 interactions with chain B- Hydrophobic interactions: B:P.126
- Hydrogen bonds: B:Y.121, B:Y.121, B:T.123, B:T.124
- Water bridges: B:G.120
MEF.15: 11 residues within 4Å:- Chain A: A.39, R.40, L.56, L.60, H.65, T.67, P.68
- Chain B: L.185
- Chain C: N.97
- Ligands: FAD.13, PEG.17
8 PLIP interactions:8 interactions with chain A- Hydrophobic interactions: A:A.39, A:L.56
- Hydrogen bonds: A:T.67
- Water bridges: A:H.65, A:H.65, A:E.66, A:T.67
- pi-Stacking: A:H.65
MEF.16: 8 residues within 4Å:- Chain C: L.118, Y.121, K.122, T.123, T.124, I.125, P.126, P.127
6 PLIP interactions:6 interactions with chain C- Hydrophobic interactions: C:P.126
- Hydrogen bonds: C:Y.121, C:Y.121, C:T.123, C:T.124
- Water bridges: C:G.120
MEF.21: 11 residues within 4Å:- Chain A: L.185
- Chain B: A.39, R.40, L.56, L.60, H.65, T.67, P.68
- Chain D: N.97
- Ligands: FAD.19, PEG.23
8 PLIP interactions:8 interactions with chain B- Hydrophobic interactions: B:A.39, B:L.56
- Hydrogen bonds: B:T.67
- Water bridges: B:H.65, B:H.65, B:E.66, B:T.67
- pi-Stacking: B:H.65
MEF.22: 8 residues within 4Å:- Chain D: L.118, Y.121, K.122, T.123, T.124, I.125, P.126, P.127
6 PLIP interactions:6 interactions with chain D- Hydrophobic interactions: D:P.126
- Hydrogen bonds: D:Y.121, D:Y.121, D:T.123, D:T.124
- Water bridges: D:G.120
- 4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
PEG.5: 2 residues within 4Å:- Chain A: Y.103
- Ligands: MEF.3
No protein-ligand interaction detected (PLIP)PEG.11: 2 residues within 4Å:- Chain B: Y.103
- Ligands: MEF.9
No protein-ligand interaction detected (PLIP)PEG.17: 2 residues within 4Å:- Chain C: Y.103
- Ligands: MEF.15
No protein-ligand interaction detected (PLIP)PEG.23: 2 residues within 4Å:- Chain D: Y.103
- Ligands: MEF.21
No protein-ligand interaction detected (PLIP)- 4 x CL: CHLORIDE ION(Non-functional Binders)
CL.6: 3 residues within 4Å:- Chain A: S.107, Y.108, Y.142
Ligand excluded by PLIPCL.12: 3 residues within 4Å:- Chain B: S.107, Y.108, Y.142
Ligand excluded by PLIPCL.18: 3 residues within 4Å:- Chain C: S.107, Y.108, Y.142
Ligand excluded by PLIPCL.24: 3 residues within 4Å:- Chain D: S.107, Y.108, Y.142
Ligand excluded by PLIP- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Koehn, E.M. et al., Folate binding site of flavin-dependent thymidylate synthase. Proc.Natl.Acad.Sci.USA (2012)
- Release Date
- 2012-10-17
- Peptides
- Thymidylate synthase thyX: 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
- 4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)
- 4 x UMP: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE(Non-covalent)
- 8 x MEF: N-({4-[(6aR)-3-amino-1-oxo-1,2,5,6,6a,7-hexahydroimidazo[1,5-f]pteridin-8(9H)-yl]phenyl}carbonyl)-L-glutamic acid(Non-covalent)
- 4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 4 x CL: CHLORIDE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Koehn, E.M. et al., Folate binding site of flavin-dependent thymidylate synthase. Proc.Natl.Acad.Sci.USA (2012)
- Release Date
- 2012-10-17
- Peptides
- Thymidylate synthase thyX: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
A