SMTL ID : 5vaj.1

BhRNase H - amide-RNA/DNA complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 2 residues within 4Å: Chain A: G.8, A.9 No protein-ligand interaction detected (PLIP) GOL.2: 3 residues within 4Å: Chain B: G.7, G.8, T.9 No protein-ligand interaction detected (PLIP) GOL.3: 2 residues within 4Å: Chain C: N.98, A.102 No protein-ligand interaction detected (PLIP) GOL.4: 7 residues within 4Å: Chain C: Y.29, L.57, V.60, H.61, R.64, E.110, A.111 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Y.29, C:L.57, C:R.64, C:R.64, C:E.110 GOL.5: 5 residues within 4Å: Chain C: H.61, R.64, Y.65, E.68, R.69 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.61, C:R.69 GOL.6: 6 residues within 4Å: Chain C: G.19, S.20, Q.21, I.26, E.28, P.45 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.19, C:E.28 Water bridges: C:S.20 GOL.7: 4 residues within 4Å: Chain C: K.89, H.118, T.119, Y.120 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.89, C:K.89, C:Y.120 Water bridges: C:H.118 GOL.11: 8 residues within 4Å: Chain D: Y.29, R.43, L.57, H.61, R.64, L.107, E.110, A.111 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Y.29, D:Y.29, D:R.43, D:R.64 GOL.12: 5 residues within 4Å: Chain D: R.64, E.110, W.114, T.117, H.118 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.64, D:R.64, D:E.110, D:T.117

4 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 5 residues within 4Å: Chain A: A.9, X.10 Chain C: D.17, E.55, N.78 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.17, C:E.55, C:E.55, H2O.4 MG.9: 3 residues within 4Å: Chain A: X.10 Chain C: D.17, D.138 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.17, C:D.138, H2O.4 MG.13: 5 residues within 4Å: Chain A: A.4, C.5 Chain D: D.17, E.55, N.78 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.17, D:E.55, D:E.55, H2O.7 MG.14: 3 residues within 4Å: Chain A: C.5 Chain D: D.17, D.138 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.17, D:D.138, H2O.6

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.10: 4 residues within 4Å: Chain B: T.4 Chain C: G.22, N.23, P.24 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.23 Water bridges: C:N.23 ACT.15: 2 residues within 4Å: Chain D: R.97, D.109 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.109 Salt bridges: D:R.97 ACT.16: 2 residues within 4Å: Chain D: H.61, Y.65 2 PLIP interactions: 2 interactions with chain D Water bridges: D:R.69 Salt bridges: D:H.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mutisya, D. et al., Amide linkages mimic phosphates in RNA interactions with proteins and are well tolerated in the guide strand of short interfering RNAs. Nucleic Acids Res. (2017)

Release Date

2017-09-13

Peptides

Ribonuclease H: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

D
B

Ribonuclease H

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