- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.45 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)
- 2 x MG: MAGNESIUM ION(Non-covalent)
MG.4: 8 residues within 4Å:- Chain A: D.11, D.72, D.132, Y.133, K.136
- Ligands: C-G.2, C-G.2, MG.5
5 PLIP interactions:2 interactions with chain A, 3 Ligand-Water interactions- Metal complexes: A:D.11, A:D.132, H2O.1, H2O.1, H2O.1
MG.5: 7 residues within 4Å:- Chain A: D.11, V.12, E.49, D.72
- Ligands: A-C-A-U.1, C-G.2, MG.4
4 PLIP interactions:4 interactions with chain A- Metal complexes: A:D.11, A:E.49, A:D.72, A:D.72
- 5 x RB: RUBIDIUM ION(Non-covalent)(Non-functional Binders)
RB.6: 8 residues within 4Å:- Chain A: D.132, Y.133, G.134, R.135, K.136
- Ligands: C-G.2, C-G.2, RB.8
No protein-ligand interaction detected (PLIP)RB.7: 2 residues within 4Å:- Chain A: K.61, N.64
No protein-ligand interaction detected (PLIP)RB.8: 5 residues within 4Å:- Chain A: E.128, D.132, K.136
- Ligands: C-G.2, RB.6
No protein-ligand interaction detected (PLIP)RB.22: 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)RB.23: 4 residues within 4Å:- Ligands: DC-DG-DA-DT-DG-DT.3, DC-DG-DA-DT-DG-DT.3, EDO.21, EDO.24
No protein-ligand interaction detected (PLIP)- 3 x CL: CHLORIDE ION(Non-functional Binders)
- 5 x GOL: GLYCEROL(Non-functional Binders)
GOL.12: 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
- Water bridges: A:P.18
GOL.13: 5 residues within 4Å:- Chain A: H.55, R.58, Y.59, R.63
- Ligands: GOL.15
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:R.58, A:R.63, A:R.63
GOL.14: 2 residues within 4Å:- Chain A: E.62, R.63
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:E.62
GOL.15: 4 residues within 4Å:- Chain A: H.55, R.58
- Ligands: CL.9, GOL.13
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:R.58
- Water bridges: A:Y.23, A:Y.23, A:R.37, A:H.55
GOL.19: 2 residues within 4Å:- Chain A: K.61, H.112
1 PLIP interactions:1 interactions with chain A- Water bridges: A:H.112
- 6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.16: 3 residues within 4Å:- Chain A: T.116, P.117, I.118
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:I.118
EDO.17: 3 residues within 4Å:- Chain A: K.83, T.113, Y.114
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:Y.114
EDO.18: 5 residues within 4Å:- Chain A: Y.59, L.60, R.63, S.65, K.67
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:S.65, A:K.67
EDO.21: 4 residues within 4Å:- Ligands: A-C-A-U.1, DC-DG-DA-DT-DG-DT.3, RB.23, EDO.24
No protein-ligand interaction detected (PLIP)EDO.24: 5 residues within 4Å:- Ligands: DC-DG-DA-DT-DG-DT.3, DC-DG-DA-DT-DG-DT.3, EDO.21, RB.23, EDO.25
No protein-ligand interaction detected (PLIP)EDO.25: 5 residues within 4Å:- Chain A: T.88
- Ligands: DC-DG-DA-DT-DG-DT.3, DC-DG-DA-DT-DG-DT.3, DC-DG-DA-DT-DG-DT.3, EDO.24
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:T.88, A:T.88
- 1 x PEG: DI(HYDROXYETHYL)ETHER(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 1.45 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)
- 2 x MG: MAGNESIUM ION(Non-covalent)
- 5 x RB: RUBIDIUM ION(Non-covalent)(Non-functional Binders)
- 3 x CL: CHLORIDE ION(Non-functional Binders)
- 5 x GOL: GLYCEROL(Non-functional Binders)
- 6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 1 x PEG: DI(HYDROXYETHYL)ETHER(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