- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.75 Å
- Oligo State
- homo-trimer
- Ligands
- 3 x MG: MAGNESIUM ION(Non-covalent)
- 3 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)
TRS.2: 14 residues within 4Å:- Chain A: Q.88, V.89, Y.90, P.91
- Chain B: Q.88, V.89, Y.90, P.91
- Chain C: Q.88, V.89, Y.90, P.91
- Ligands: TRS.6, TRS.10
8 PLIP interactions:4 interactions with chain B, 2 interactions with chain C, 2 interactions with chain A- Hydrogen bonds: B:Q.88, B:V.89, C:Q.88, A:Q.88
- Water bridges: B:G.78, B:V.89, C:V.89, A:V.89
TRS.6: 14 residues within 4Å:- Chain A: Q.88, V.89, Y.90, P.91
- Chain B: Q.88, V.89, Y.90, P.91
- Chain C: Q.88, V.89, Y.90, P.91
- Ligands: TRS.2, TRS.10
8 PLIP interactions:2 interactions with chain B, 4 interactions with chain C, 2 interactions with chain A- Hydrogen bonds: B:Q.88, C:Q.88, C:V.89, A:Q.88
- Water bridges: B:V.89, C:G.78, C:V.89, A:V.89
TRS.10: 14 residues within 4Å:- Chain A: Q.88, V.89, Y.90, P.91
- Chain B: Q.88, V.89, Y.90, P.91
- Chain C: Q.88, V.89, Y.90, P.91
- Ligands: TRS.2, TRS.6
8 PLIP interactions:2 interactions with chain B, 2 interactions with chain C, 4 interactions with chain A- Hydrogen bonds: B:Q.88, C:Q.88, A:Q.88, A:V.89
- Water bridges: B:V.89, C:V.89, A:G.78, A:V.89
- 3 x DUP: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE(Non-covalent)
DUP.3: 17 residues within 4Å:- Chain A: I.76, G.92, V.93, I.94, D.95, Y.98, E.101, I.102, K.103, M.105
- Chain C: G.78, R.79, S.80, S.81, Q.123
- Ligands: MG.1, UMP.4
16 PLIP interactions:5 interactions with chain A, 11 interactions with chain C- Hydrophobic interactions: A:Y.98
- Hydrogen bonds: A:D.95, A:K.103, A:K.103, C:R.79, C:S.80, C:S.80, C:S.80, C:S.81, C:R.120, C:Q.123
- Water bridges: A:M.105, C:R.79, C:S.81, C:S.81
- Salt bridges: C:R.79
DUP.7: 17 residues within 4Å:- Chain A: G.78, R.79, S.80, S.81, Q.123
- Chain B: I.76, G.92, V.93, I.94, D.95, Y.98, E.101, I.102, K.103, M.105
- Ligands: MG.5, UMP.8
16 PLIP interactions:5 interactions with chain B, 11 interactions with chain A- Hydrophobic interactions: B:Y.98
- Hydrogen bonds: B:D.95, B:K.103, B:K.103, A:R.79, A:S.80, A:S.80, A:S.80, A:S.81, A:R.120, A:Q.123
- Water bridges: B:M.105, A:R.79, A:S.81, A:S.81
- Salt bridges: A:R.79
DUP.11: 17 residues within 4Å:- Chain B: G.78, R.79, S.80, S.81, Q.123
- Chain C: I.76, G.92, V.93, I.94, D.95, Y.98, E.101, I.102, K.103, M.105
- Ligands: MG.9, UMP.12
16 PLIP interactions:11 interactions with chain B, 5 interactions with chain C- Hydrogen bonds: B:R.79, B:S.80, B:S.80, B:S.80, B:S.81, B:R.120, B:Q.123, C:D.95, C:K.103, C:K.103
- Water bridges: B:R.79, B:S.81, B:S.81, C:M.105
- Salt bridges: B:R.79
- Hydrophobic interactions: C:Y.98
- 3 x UMP: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE(Non-covalent)
UMP.4: 14 residues within 4Å:- Chain A: G.92, V.93, I.94, D.95, Y.98, E.101, I.102, K.103, M.105
- Chain C: R.79, S.80, Q.123
- Ligands: MG.1, DUP.3
10 PLIP interactions:7 interactions with chain A, 3 interactions with chain C- Hydrophobic interactions: A:I.94, A:Y.98
- Hydrogen bonds: A:D.95, A:D.95, A:K.103, A:K.103, C:S.80, C:S.80, C:Q.123
- Water bridges: A:M.105
UMP.8: 14 residues within 4Å:- Chain A: R.79, S.80, Q.123
- Chain B: G.92, V.93, I.94, D.95, Y.98, E.101, I.102, K.103, M.105
- Ligands: MG.5, DUP.7
10 PLIP interactions:7 interactions with chain B, 3 interactions with chain A- Hydrophobic interactions: B:I.94, B:Y.98
- Hydrogen bonds: B:D.95, B:D.95, B:K.103, B:K.103, A:S.80, A:S.80, A:Q.123
- Water bridges: B:M.105
UMP.12: 14 residues within 4Å:- Chain B: R.79, S.80, Q.123
- Chain C: G.92, V.93, I.94, D.95, Y.98, E.101, I.102, K.103, M.105
- Ligands: MG.9, DUP.11
10 PLIP interactions:3 interactions with chain B, 7 interactions with chain C- Hydrogen bonds: B:S.80, B:S.80, B:Q.123, C:D.95, C:D.95, C:K.103, C:K.103
- Hydrophobic interactions: C:I.94, C:Y.98
- Water bridges: C:M.105
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Barabas, O. et al., Structural Snapshots of Enzyme-Catalysed Phosphate Ester Hydrolysis Directly Visualize In-line Attack and Inversion. to be published
- Release Date
- 2011-10-12
- Peptides
- DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDO HYDROLASE: ABC
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.75 Å
- Oligo State
- homo-trimer
- Ligands
- 3 x MG: MAGNESIUM ION(Non-covalent)
- 3 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)
- 3 x DUP: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE(Non-covalent)
- 3 x UMP: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Barabas, O. et al., Structural Snapshots of Enzyme-Catalysed Phosphate Ester Hydrolysis Directly Visualize In-line Attack and Inversion. to be published
- Release Date
- 2011-10-12
- Peptides
- DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDO HYDROLASE: ABC
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
A