SMTL ID : 6m6r.1

Crystal structure of Caenorhabditis elegans Dicer-related helicase 3 (DRH-3) C-terminal domain with 5'-ppp 8-mer ssRNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-dimer

Ligands

2 x GTP- G- C- C- G- C- C- C: RNA (5'-R(*(GTP)P*GP*CP*CP*GP*CP*CP*C)-3')(Non-covalent)

GTP-G-C-C-G-C-C-C.1: 23 residues within 4Å: Chain A: S.32, N.33, K.50, S.54, K.55, Y.56, R.78, Y.80, Q.89, K.110, W.111, S.112 Chain B: Y.56, N.61, K.93 Ligands: GTP-G-C-C-G-C-C-C.3, GTP-G-C-C-G-C-C-C.3, GTP-G-C-C-G-C-C-C.3, GTP-G-C-C-G-C-C-C.3, GTP-G-C-C-G-C-C-C.3, GTP-G-C-C-G-C-C-C.3, GTP-G-C-C-G-C-C-C.3, GTP-G-C-C-G-C-C-C.3 19 PLIP interactions: 16 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.33, A:S.54, A:S.54, A:K.55, A:R.78, A:Y.80, A:Y.80, A:Q.89, A:Q.89 Water bridges: A:R.78, A:R.78 Salt bridges: A:K.50, A:K.50, A:K.50, A:R.78, A:R.78, B:K.93, B:K.93, B:K.93 GTP-G-C-C-G-C-C-C.3: 23 residues within 4Å: Chain A: Y.56, N.61, K.93 Chain B: S.32, N.33, K.50, S.54, K.55, Y.56, R.78, Y.80, Q.89, K.110, W.111, S.112 Ligands: GTP-G-C-C-G-C-C-C.1, GTP-G-C-C-G-C-C-C.1, GTP-G-C-C-G-C-C-C.1, GTP-G-C-C-G-C-C-C.1, GTP-G-C-C-G-C-C-C.1, GTP-G-C-C-G-C-C-C.1, GTP-G-C-C-G-C-C-C.1, GTP-G-C-C-G-C-C-C.1 19 PLIP interactions: 16 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:N.33, B:S.54, B:S.54, B:K.55, B:R.78, B:Y.80, B:Y.80, B:Q.89, B:Q.89 Water bridges: B:R.78, B:R.78 Salt bridges: B:K.50, B:K.50, B:K.50, B:R.78, B:R.78, A:K.93, A:K.93, A:K.93

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.14, C.17, C.69, C.72 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.14, A:C.17, A:C.69, A:C.72 ZN.4: 4 residues within 4Å: Chain B: C.14, C.17, C.69, C.72 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.14, B:C.17, B:C.69, B:C.72

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, K. et al., Insights into the structure and RNA-binding specificity of Caenorhabditis elegans Dicer-related helicase 3 (DRH-3). Nucleic Acids Res. (2021)

Release Date

2021-03-17

Peptides

Dicer Related Helicase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Dicer Related Helicase

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