- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.46 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)
- 3 x K: POTASSIUM ION(Non-covalent)(Non-functional Binders)
K.6: 7 residues within 4Å:- Chain A: D.138, Y.139, G.140, R.141, K.142
- Ligands: C-G.2, C-G.2
3 PLIP interactions:1 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:D.138, H2O.1, H2O.4
K.7: 5 residues within 4Å:- Chain A: T.129, E.134, K.142
- Ligands: A-C-A-U.1, C-G.2
1 PLIP interactions:1 interactions with chain A- Metal complexes: A:E.134
K.24: 3 residues within 4Å:- Ligands: A-C-A-U.1, DC-DG-DA-DT-DG-DT.3, EDO.25
No protein-ligand interaction detected (PLIP)- 3 x IOD: IODIDE ION(Non-functional Binders)
- 9 x GOL: GLYCEROL(Non-functional Binders)
GOL.11: 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
- Water bridges: A:P.24
GOL.12: 6 residues within 4Å:- Chain A: Y.29, L.57, V.60, H.61, R.64, A.111
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:Y.29, A:H.61, A:R.64
GOL.13: 5 residues within 4Å:- Chain A: H.61, R.64, Y.65, E.68, R.69
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:R.69, A:R.69
- Water bridges: A:R.64
GOL.14: 7 residues within 4Å:- Chain A: K.89, L.115, N.116, T.117, H.118, T.119
- Ligands: GOL.22
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:L.115, A:H.118
GOL.20: 4 residues within 4Å:- Chain A: K.90, R.97, D.109, E.112
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:R.97, A:D.109, A:E.112
- Water bridges: A:K.90, A:E.113
GOL.21: 3 residues within 4Å:- Chain A: V.96, R.97
- Ligands: EDO.16
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:R.97
GOL.22: 6 residues within 4Å:- Chain A: K.89, L.115, H.118, T.119, Y.120
- Ligands: GOL.14
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:K.89, A:L.115, A:Y.120, A:Y.120
GOL.23: 6 residues within 4Å:- Chain A: I.83, K.87, I.124, L.125, K.126
- Ligands: IOD.8
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:K.87, A:K.126
- Water bridges: A:K.126
GOL.26: 5 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, EDO.25
No protein-ligand interaction detected (PLIP)- 6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.15: 5 residues within 4Å:- Chain A: 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
EDO.16: 7 residues within 4Å:- Chain A: S.93, T.94, L.95, V.96, R.97, W.105
- Ligands: GOL.21
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:S.93
EDO.17: 3 residues within 4Å:- Chain A: K.67, E.68, N.70
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:E.68, A:N.70
EDO.18: 4 residues within 4Å:- Chain A: R.97, N.98, E.99, A.102
1 PLIP interactions:1 interactions with chain A- Water bridges: A:A.102
EDO.19: 6 residues within 4Å:- Chain A: P.24, L.95, V.96, N.98, E.100, T.101
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:N.98, A:N.98
EDO.25: 4 residues within 4Å:- Ligands: DC-DG-DA-DT-DG-DT.3, DC-DG-DA-DT-DG-DT.3, K.24, GOL.26
No protein-ligand interaction detected (PLIP)- 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 1.46 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)
- 3 x K: POTASSIUM ION(Non-covalent)(Non-functional Binders)
- 3 x IOD: IODIDE ION(Non-functional Binders)
- 9 x GOL: GLYCEROL(Non-functional Binders)
- 6 x EDO: 1,2-ETHANEDIOL(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