SMTL ID : 6h57.1

Crystal structure of S. cerevisiae DEAH-box RNA helicase Dhr1, essential for small ribosomal subunit biogenesis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

14 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 6 residues within 4Å: Chain A: F.1000, E.1146, M.1147, P.1148, P.1149 Ligands: EDO.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.1147 Water bridges: A:K.1150 EDO.2: 7 residues within 4Å: Chain A: P.1149, K.1150, Y.1151, D.1172, I.1173, A.1174 Ligands: EDO.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.1150, A:Y.1151, A:Y.1151 EDO.3: 6 residues within 4Å: Chain A: H.405, H.406, N.407, D.408, K.552, K.554 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.405, A:K.552, A:K.554 EDO.4: 9 residues within 4Å: Chain A: L.1099, R.1216, S.1219, T.1220, N.1223, D.1224, K.1226, I.1227, G.1228 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.1216, A:S.1219, A:G.1228 EDO.5: 4 residues within 4Å: Chain A: M.401, H.405, F.433, Y.441 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.441 EDO.6: 5 residues within 4Å: Chain A: Q.884, G.887, L.889, D.890, L.1186 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.884 Water bridges: A:N.891 EDO.7: 4 residues within 4Å: Chain A: R.640, L.729, Y.730, V.731 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.640, A:L.729, A:V.731 EDO.8: 4 residues within 4Å: Chain A: K.878, Q.881, Y.885 Ligands: EDO.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.885 EDO.9: 7 residues within 4Å: Chain A: K.878, Q.881, L.882, Y.885, R.910, D.1090 Ligands: EDO.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.878, A:K.878, A:L.882, A:R.910 EDO.10: 8 residues within 4Å: Chain A: E.415, T.416, G.417, S.418, G.419, K.420, T.421, T.422 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.415, A:G.417, A:S.418, A:G.419, A:K.420, A:T.422 EDO.11: 3 residues within 4Å: Chain A: T.896, E.897, D.898 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.896, A:E.897, A:D.898 EDO.12: 4 residues within 4Å: Chain A: E.545, N.546, P.547, I.548 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.545, A:N.546 EDO.13: 5 residues within 4Å: Chain A: A.1122, T.1123, T.1125, D.1130, C.1131 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.1123 EDO.14: 4 residues within 4Å: Chain A: E.500, H.503, D.504, K.509 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.503, A:K.509 Water bridges: A:E.500, A:D.504, A:D.504, A:K.509

1 x MG: MAGNESIUM ION(Non-covalent)

MG.15: 3 residues within 4Å: Chain A: Q.881, Q.884, E.893 No protein-ligand interaction detected (PLIP)

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.16: 2 residues within 4Å: Chain A: D.1002, T.1169 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain A: G.474, Y.475 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain A: P.871, D.872 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain A: L.1006, N.1168, T.1169 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roychowdhury, A. et al., The DEAH-box RNA helicase Dhr1 contains a remarkable carboxyl terminal domain essential for small ribosomal subunit biogenesis. Nucleic Acids Res. (2019)

Release Date

2019-06-19

Peptides

Probable ATP-dependent RNA helicase DHR1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Probable ATP-dependent RNA helicase DHR1

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