- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.29 Å
- Oligo State
- monomer
- Ligands
- 1 x A- C- A- U: RNA (5'-R(*AP*CP*AP*U)-3')(Non-covalent)
- 1 x C- G: RNA (5'-R(P*CP*G)-3')(Non-covalent)
- 1 x DC- DG- DA- DT- DG- DT: DNA (5'-D(*CP*GP*AP*TP*GP*T)-3')(Non-covalent)
- 2 x MG: MAGNESIUM ION(Non-covalent)
- 3 x K: POTASSIUM ION(Non-covalent)(Non-functional Binders)
K.6: 8 residues within 4Å:- Chain A: D.138, Y.139, G.140, R.141, K.142
- Ligands: C-G.2, C-G.2, MG.4
3 PLIP interactions:1 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:D.138, H2O.2, H2O.7
K.20: 5 residues within 4Å:- Chain A: D.78, T.129, E.134
- Ligands: A-C-A-U.1, C-G.2
No protein-ligand interaction detected (PLIP)K.21: 2 residues within 4Å:- Ligands: DC-DG-DA-DT-DG-DT.3, DC-DG-DA-DT-DG-DT.3
No protein-ligand interaction detected (PLIP)- 4 x IOD: IODIDE ION(Non-functional Binders)
IOD.7: 4 residues within 4Å:- Chain A: Y.29, R.43, L.57, L.107
Ligand excluded by PLIPIOD.8: 4 residues within 4Å:- Chain A: Q.80, I.83, K.126
- Ligands: PGE.19
Ligand excluded by PLIPIOD.9: 4 residues within 4Å:- Chain A: I.10, P.74, P.123, L.125
Ligand excluded by PLIPIOD.10: 2 residues within 4Å:- Chain A: K.67, H.118
Ligand excluded by PLIP- 4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.11: 3 residues within 4Å:- Chain A: K.89, T.119, Y.120
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:K.89, A:Y.120, A:Y.120
EDO.12: 3 residues within 4Å:- Chain A: T.94
- Ligands: DC-DG-DA-DT-DG-DT.3, DC-DG-DA-DT-DG-DT.3
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:T.94
EDO.13: 3 residues within 4Å:- Chain A: Q.21, I.26, P.45
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:Q.21
- Water bridges: A:P.45
EDO.14: 8 residues within 4Å:- Chain A: W.11, E.12, S.13, D.33, T.34, L.40, K.73
- Ligands: GOL.18
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:S.13, A:T.34, A:K.73
- Water bridges: A:D.33
- 5 x GOL: GLYCEROL(Non-functional Binders)
GOL.15: 3 residues within 4Å:- Chain A: H.61, R.64
- Ligands: GOL.16
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:R.64
- Water bridges: A:Y.29, A:H.61
GOL.16: 6 residues within 4Å:- Chain A: H.61, R.64, Y.65, E.68, R.69
- Ligands: GOL.15
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:R.64, A:R.64, A:R.69, A:R.69
GOL.17: 7 residues within 4Å:- Chain A: P.24, I.48, L.95, V.96, N.98, E.100, T.101
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:N.98, A:E.100
GOL.18: 7 residues within 4Å:- Chain A: L.40, Y.65, L.66, R.69, S.71, K.73
- Ligands: EDO.14
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:S.71, A:K.73, A:K.73
- Water bridges: A:D.33
GOL.22: 5 residues within 4Å:- Chain A: G.22, N.23, P.24
- Ligands: DC-DG-DA-DT-DG-DT.3, DC-DG-DA-DT-DG-DT.3
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:N.23, A:P.24
- 1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Samara, N.L. et al., Cation trafficking propels RNA hydrolysis. Nat. Struct. Mol. Biol. (2018)
- Release Date
- 2018-08-15
- Peptides
- Ribonuclease H: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.29 Å
- Oligo State
- monomer
- Ligands
- 1 x A- C- A- U: RNA (5'-R(*AP*CP*AP*U)-3')(Non-covalent)
- 1 x C- G: RNA (5'-R(P*CP*G)-3')(Non-covalent)
- 1 x DC- DG- DA- DT- DG- DT: DNA (5'-D(*CP*GP*AP*TP*GP*T)-3')(Non-covalent)
- 2 x MG: MAGNESIUM ION(Non-covalent)
- 3 x K: POTASSIUM ION(Non-covalent)(Non-functional Binders)
- 4 x IOD: IODIDE ION(Non-functional Binders)
- 4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 5 x GOL: GLYCEROL(Non-functional Binders)
- 1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Samara, N.L. et al., Cation trafficking propels RNA hydrolysis. Nat. Struct. Mol. Biol. (2018)
- Release Date
- 2018-08-15
- Peptides
- Ribonuclease H: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A