- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.47 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.132, Y.133, G.134, R.135, K.136
- 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.132, H2O.2, H2O.7
K.19: 5 residues within 4Å:- Chain A: D.72, T.123, E.128
- Ligands: A-C-A-U.1, C-G.2
No protein-ligand interaction detected (PLIP)K.20: 3 residues within 4Å:- Ligands: A-C-A-U.1, 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.23, R.37, L.51, L.101
Ligand excluded by PLIPIOD.8: 4 residues within 4Å:- Chain A: Q.74, I.77, K.120
- Ligands: PGE.18
Ligand excluded by PLIPIOD.9: 4 residues within 4Å:- Chain A: I.4, P.68, P.117, L.119
Ligand excluded by PLIPIOD.10: 2 residues within 4Å:- Chain A: K.61, H.112
Ligand excluded by PLIP- 4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.11: 3 residues within 4Å:- Chain A: K.83, T.113, Y.114
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:K.83, A:Y.114, A:Y.114
EDO.12: 3 residues within 4Å:- Chain A: T.88
- 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.88
EDO.13: 4 residues within 4Å:- Chain A: Q.15, I.20, P.39, P.41
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:Q.15
- Water bridges: A:P.39
EDO.14: 8 residues within 4Å:- Chain A: W.5, E.6, S.7, D.27, T.28, K.29, L.34, K.67
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:S.7, A:K.29, A:K.29, A:K.67
- Water bridges: A:D.27
- 4 x GOL: GLYCEROL(Non-functional Binders)
GOL.15: 3 residues within 4Å:- Chain A: H.55, R.58
- Ligands: GOL.16
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:R.58
- Water bridges: A:Y.23, A:H.55
GOL.16: 6 residues within 4Å:- Chain A: H.55, R.58, Y.59, E.62, R.63
- Ligands: GOL.15
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:R.58, A:R.58, A:R.63
GOL.17: 7 residues within 4Å:- Chain A: P.18, I.42, L.89, V.90, N.92, E.94, T.95
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:N.92, A:E.94
GOL.21: 5 residues within 4Å:- Chain A: G.16, N.17, P.18
- 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.17, A:P.18
- 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 1.47 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)
- 4 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