SMTL ID : 8dzk.3 (4 other biounits)

Dbr1 in complex with 5-mer cleavage product

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x G46- U- G- U- U: RNA (5'-R(P*(G46)P*UP*GP*UP*U)-3')(Non-covalent)

G46-U-G-U-U.1: 23 residues within 4Å: Chain A: C.16, H.18, D.47, K.61, Y.66, N.92, H.93, I.134, K.136, F.138, F.157, H.158, G.203, F.204, K.206, D.207, L.211, H.232, M.233, H.234, K.251 Ligands: FE2.2, ZN.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.47, A:N.92, A:H.232, A:H.234 Water bridges: A:G.212 Salt bridges: A:D.207

1 x FE2: FE (II) ION(Non-covalent)

FE2.2: 6 residues within 4Å: Chain A: D.47, N.92, H.182, H.232 Ligands: G46-U-G-U-U.1, ZN.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.47, A:H.182, A:H.232

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain A: C.16, H.18, D.47, H.234 Ligands: G46-U-G-U-U.1, FE2.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.16, A:H.18, A:D.47, A:H.234

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain A: R.52, N.97, H.101, P.148 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.97 Water bridges: A:R.52, A:R.52 Salt bridges: A:R.52, A:H.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Clark, N.E. et al., Crystal Structure of the RNA Lariat Debranching Enzyme Dbr1 with Hydrolyzed Phosphorothioate RNA Product. Biochemistry (2022)

Release Date

2022-08-24

Peptides

RNA lariat debranching enzyme, putative: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

RNA lariat debranching enzyme, putative

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