SMTL ID : 4pei.1 (4 other biounits)

Dbr1 in complex with synthetic branched RNA analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

1 x A- C- A: RNA (5'-R(*UP*AP*AP*CP*A)-3')(Non-covalent)

A-C-A.1: 15 residues within 4Å: Chain A: H.18, Q.49, K.61, V.62, P.63, Y.66, N.92, H.93, I.134, K.136, F.157, H.158, H.232, K.251 Ligands: G46.2 Protein-ligand interaction information (PLIP) not available

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

G46.2: 15 residues within 4Å: Chain A: H.18, D.47, N.92, H.93, G.203, F.204, D.207, L.211, H.232, M.233, H.234 Ligands: A-C-A.1, A-C-A.1, NI.3, GOL.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.92, A:G.203, A:M.233, A:H.234 Salt bridges: A:D.207

1 x NI: NICKEL (II) ION(Non-covalent)

NI.3: 5 residues within 4Å: Chain A: D.47, N.92, H.182, H.232 Ligands: G46.2 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.47, A:H.182, A:H.232, H2O.2, G46.2

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

SO4.4: 5 residues within 4Å: Chain A: R.52, Y.59, N.97, H.101, P.148 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.97 Water bridges: A:R.52, A:R.52, A:R.52 Salt bridges: A:R.52, A:H.101

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: M.69, G.70, D.71, H.73, L.74 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.70, A:H.73 Water bridges: A:K.20, A:D.71 GOL.6: 8 residues within 4Å: Chain A: Y.135, K.136, D.183, L.211, G.212, S.213, H.232 Ligands: G46.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.136, A:G.212 Water bridges: A:Y.135, A:K.136, A:G.212

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Montemayor, E.J. et al., Structural basis of lariat RNA recognition by the intron debranching enzyme Dbr1. Nucleic Acids Res. (2014)

Release Date

2014-08-27

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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