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

Dbr1 in complex with synthetic linear RNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x A- A2P- C- A: RNA (5'-R(*CP*UP*AP*(A2P)P*AP*CP*AP*A)-3')(Non-covalent)

A-A2P-C-A.1: 21 residues within 4Å: Chain A: H.18, D.47, Q.49, K.61, P.63, Y.66, N.92, H.93, I.134, K.136, F.157, H.158, G.203, F.204, D.207, L.211, H.232, M.233, H.234, K.251 Ligands: MN.2 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:D.47, A:N.92, A:H.232, A:H.232, A:K.251 Water bridges: A:H.18, A:H.18, A:Q.49, A:H.232, A:H.232, A:K.251 Salt bridges: A:H.18, A:H.93, A:H.232, A:H.234, A:H.234 pi-Stacking: A:H.18, A:H.18, A:Y.66, A:Y.66

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 5 residues within 4Å: Chain A: D.47, N.92, H.182, H.232 Ligands: A-A2P-C-A.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.47, A:H.182, A:H.232, H2O.8

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

SO4.3: 4 residues within 4Å: Chain A: R.52, N.97, H.101, P.148 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.97 Water bridges: A:R.52, A:R.52, A:R.52, A:R.52, A:R.52, A:Y.59 Salt bridges: A:R.52, A:H.101

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: Q.165, S.300, I.301, S.302 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.301, A:S.302

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

Related Entries With Identical Sequence