SMTL ID : 5k77.1 (4 other biounits)

Dbr1 in complex with 7-mer branched RNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

monomer

Ligands

1 x A- A- C- A: branch 1 of branched RNA 5'-UAA(-2'GU)CA-3'(Non-covalent)

A-A-C-A.1: 17 residues within 4Å: Chain A: H.16, Q.47, K.59, V.60, P.61, Y.64, N.90, I.132, K.134, F.155, H.156, H.230, H.232, K.249 Ligands: G-U.2, G-U.2, SO4.6 Protein-ligand interaction information (PLIP) not available

1 x G- U: brnch 2 of branched RNA 5'-UAA(-2'GU)CA-3'(Non-covalent)

G-U.2: 16 residues within 4Å: Chain A: H.16, D.45, N.90, G.201, F.202, K.204, D.205, L.209, H.230, M.231, H.232 Ligands: A-A-C-A.1, A-A-C-A.1, ZN.3, FE2.4, OH.10 Protein-ligand interaction information (PLIP) not available

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 8 residues within 4Å: Chain A: C.14, H.16, D.45, H.230, H.232 Ligands: G-U.2, FE2.4, OH.10 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:C.14, A:H.16, A:D.45, A:H.232, OH.10

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

FE2.4: 7 residues within 4Å: Chain A: D.45, N.90, H.180, H.230 Ligands: G-U.2, ZN.3, OH.10 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.45, A:H.180, A:H.230, OH.10

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

SO4.5: 5 residues within 4Å: Chain A: R.50, D.54, N.95, H.99, P.146 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.95 Water bridges: A:Y.51, A:Y.51 Salt bridges: A:R.50, A:H.99 SO4.6: 5 residues within 4Å: Chain A: K.18, Y.64, K.249, Y.252 Ligands: A-A-C-A.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.252, A:Y.252 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 SO4.8: 3 residues within 4Å: Chain A: Y.51, Y.74, T.332 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.74 SO4.9: 2 residues within 4Å: Chain A: K.289, T.338 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.289

1 x OH: HYDROXIDE ION(Non-covalent)

OH.10: 9 residues within 4Å: Chain A: C.14, H.16, D.45, H.180, H.230, H.232 Ligands: G-U.2, ZN.3, FE2.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Clark, N.E. et al., Metal dependence and branched RNA cocrystal structures of the RNA lariat debranching enzyme Dbr1. Proc. Natl. Acad. Sci. U.S.A. (2016)

Release Date

2016-12-07

Peptides

RNA lariat debranching enzyme, putative: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RNA lariat debranching enzyme, putative

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