SMTL ID : 5k78.3 (4 other biounits)

Dbr1 in complex with 16-mer branched RNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.64 Å

Oligo State

monomer

Ligands

1 x G- U- A- U- G- U: branch 2 of branched RNA 5'-UACUAA(2'-GUAUGU)CAAGU-3'(Non-covalent)

G-U-A-U-G-U.1: 24 residues within 4Å: Chain A: H.16, D.45, N.90, Q.194, R.197, F.198, Q.199, G.201, F.202, D.205, L.209, H.230, M.231, H.232, C.233, E.234, K.249, Y.252, N.254 Chain B: A.5, A.6, C.7 Ligands: FE2.2, ZN.3 Protein-ligand interaction information (PLIP) not available

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

FE2.2: 6 residues within 4Å: Chain A: D.45, N.90, H.180, H.230 Ligands: G-U-A-U-G-U.1, ZN.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.45, A:H.180, A:H.230

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 7 residues within 4Å: Chain A: C.14, H.16, D.45, H.230, H.232 Ligands: G-U-A-U-G-U.1, FE2.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.14, A:H.16, A:D.45, A:H.232

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

SO4.4: 6 residues within 4Å: Chain A: R.50, D.54, Y.57, N.95, H.99, P.146 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.54, A:N.95 Salt bridges: A:R.50, A:H.99 SO4.5: 2 residues within 4Å: Chain A: S.172, Q.173 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.173, A:Q.173, A:Q.173 SO4.6: 4 residues within 4Å: Chain A: K.18, Y.64, K.249 Chain B: A.6 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.18, A:K.249 SO4.7: 2 residues within 4Å: Chain A: K.320, Y.321 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.320

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Clark, N.E. et al., The RNA lariat debranching enzyme Dbr1: metal dependence and branched RNA co-crystal structures. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-12-07

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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