- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.39 Å
- Oligo State
- monomer
- Ligands
- 1 x A- C- A- U: 5'-R(*AP*CP*AP*U)-3' portion of cleaved RNA 5'-R(*AP*CP*AP*UP*CP*G)-3'(Non-covalent)
- 1 x C- G: 5'-R(P*CP*G)-3' portion of cleaved RNA (5'-R(*AP*CP*AP*UP*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)
- 4 x MN: MANGANESE (II) ION(Non-covalent)
- 3 x IOD: IODIDE ION(Non-functional Binders)
- 4 x GOL: GLYCEROL(Non-functional Binders)
GOL.8: 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
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:N.23, A:N.23
- Water bridges: A:P.24
GOL.9: 6 residues within 4Å:- Chain A: H.61, R.64, Y.65, E.68, R.69
- Ligands: GOL.10
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:R.69, A:R.69
- Water bridges: A:R.64, A:E.68
GOL.10: 4 residues within 4Å:- Chain A: H.61, R.64
- Ligands: IOD.5, GOL.9
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:H.61, A:R.64
- Water bridges: A:Y.29, A:H.61
GOL.14: 6 residues within 4Å:- Chain A: L.40, Y.65, L.66, R.69, S.71, K.73
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:S.71, A:K.73
- 5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.11: 3 residues within 4Å:- Chain A: K.89, T.119, Y.120
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:Y.120, A:Y.120
EDO.12: 4 residues within 4Å:- Chain A: T.94
- Ligands: DC-DG-DA-DT-DG-DT.3, DC-DG-DA-DT-DG-DT.3, DC-DG-DA-DT-DG-DT.3
No protein-ligand interaction detected (PLIP)EDO.13: 1 residues within 4Å:- Chain A: R.97
No protein-ligand interaction detected (PLIP)EDO.15: 2 residues within 4Å:- Chain A: R.72, E.121
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:R.72, A:E.121
- Water bridges: A:E.121
EDO.16: 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
- 2 x K: POTASSIUM ION(Non-covalent)(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 1.39 Å
- Oligo State
- monomer
- Ligands
- 1 x A- C- A- U: 5'-R(*AP*CP*AP*U)-3' portion of cleaved RNA 5'-R(*AP*CP*AP*UP*CP*G)-3'(Non-covalent)
- 1 x C- G: 5'-R(P*CP*G)-3' portion of cleaved RNA (5'-R(*AP*CP*AP*UP*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)
- 4 x MN: MANGANESE (II) ION(Non-covalent)
- 3 x IOD: IODIDE ION(Non-functional Binders)
- 4 x GOL: GLYCEROL(Non-functional Binders)
- 5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 2 x K: POTASSIUM ION(Non-covalent)(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