- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.81 Å
- Oligo State
- hetero-1-1-mer
- Ligands
- 1 x APC- G- U: RNA (5'-D(*(APC))-R(P*GP*U)-3')(Non-covalent)
- 7 x GOL: GLYCEROL(Non-functional Binders)
GOL.2: 4 residues within 4Å:- Chain A: Y.53, H.60, S.99, T.100
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:S.99
- Water bridges: A:R.104
GOL.3: 3 residues within 4Å:- Chain A: Q.45, N.65, V.71
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:Q.45, A:N.65
- Water bridges: A:A.66, A:A.66, A:D.67
GOL.4: 4 residues within 4Å:- Chain A: R.104, M.105, V.106, N.118
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:V.106, A:N.118
- Hydrogen bonds: A:V.106
GOL.5: 1 residues within 4Å:- Chain A: H.267
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:H.267
GOL.12: 4 residues within 4Å:- Chain B: S.46, A.47, E.48, F.101
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:S.46, B:A.47, B:E.48, B:E.48
GOL.13: 4 residues within 4Å:- Chain A: N.23
- Chain B: R.142, D.143, R.146
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:R.146, B:R.146
- Water bridges: B:S.139, B:R.142
GOL.14: 5 residues within 4Å:- Chain B: I.112, N.113, M.114, Q.115, W.125
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:I.112, B:N.113, B:M.114
- Water bridges: B:W.125
- 5 x CL: CHLORIDE ION(Non-functional Binders)
CL.6: 5 residues within 4Å:- Chain A: G.9, G.77, A.78, R.79, C.80
Ligand excluded by PLIPCL.7: 4 residues within 4Å:- Chain A: M.142, R.143, H.183, R.185
Ligand excluded by PLIPCL.8: 3 residues within 4Å:- Chain A: N.158, N.191, R.210
Ligand excluded by PLIPCL.15: 2 residues within 4Å:- Chain B: S.62, R.63
Ligand excluded by PLIPCL.16: 1 residues within 4Å:- Chain A: P.51
Ligand excluded by PLIP- 3 x MG: MAGNESIUM ION(Non-covalent)
MG.9: 5 residues within 4Å:- Chain B: G.40, E.54, E.57
- Ligands: APC-G-U.1, MG.10
5 PLIP interactions:1 interactions with chain B, 4 Ligand-Water interactions- Metal complexes: B:E.54, H2O.6, H2O.7, H2O.9, H2O.11
MG.10: 7 residues within 4Å:- Chain B: E.54, E.57, E.58, E.121
- Ligands: APC-G-U.1, MG.9, MG.11
5 PLIP interactions:4 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:E.54, B:E.57, B:E.58, B:E.121, H2O.9
MG.11: 7 residues within 4Å:- Chain B: Q.38, G.39, E.54, E.58, E.121
- Ligands: APC-G-U.1, MG.10
4 PLIP interactions:3 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:Q.38, B:E.58, B:E.121, H2O.8
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Gao, A. et al., Structural and kinetic insights into stimulation of RppH-dependent RNA degradation by the metabolic enzyme DapF. Nucleic Acids Res. (2018)
- Release Date
- 2018-05-23
- Peptides
- Diaminopimelate epimerase: A
RNA pyrophosphohydrolase: B - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.81 Å
- Oligo State
- hetero-1-1-mer
- Ligands
- 1 x APC- G- U: RNA (5'-D(*(APC))-R(P*GP*U)-3')(Non-covalent)
- 7 x GOL: GLYCEROL(Non-functional Binders)
- 5 x CL: CHLORIDE ION(Non-functional Binders)
- 3 x MG: MAGNESIUM ION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Gao, A. et al., Structural and kinetic insights into stimulation of RppH-dependent RNA degradation by the metabolic enzyme DapF. Nucleic Acids Res. (2018)
- Release Date
- 2018-05-23
- Peptides
- Diaminopimelate epimerase: A
RNA pyrophosphohydrolase: B - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B