SMTL ID : 5o1x.1

Structure of Nrd1 RNA binding domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 3 residues within 4Å: Chain A: Y.49, R.96, E.100 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.170 EDO.2: 3 residues within 4Å: Chain A: Y.18, K.72, E.76 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.72 Water bridges: A:A.68, A:K.72 EDO.3: 8 residues within 4Å: Chain A: F.54, F.90, R.117, W.118, G.119, V.120, R.125, Y.130 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.117, A:R.117, A:V.120, A:V.120, A:R.125 EDO.4: 5 residues within 4Å: Chain A: Y.18, E.21, N.27, P.28, H.29 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.21, A:E.21, A:N.27 EDO.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.6: 5 residues within 4Å: Chain A: I.81, N.83, R.86, H.88, F.90 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.83, A:R.86, A:H.88 EDO.7: 3 residues within 4Å: Chain A: R.117, Y.130 Ligands: SCN.11 No protein-ligand interaction detected (PLIP)

8 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.8: 2 residues within 4Å: Chain A: N.69, V.70 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.66 SCN.9: 5 residues within 4Å: Chain A: D.44, M.139, V.164, T.165 Ligands: SCN.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.165 SCN.10: 4 residues within 4Å: Chain A: P.59, M.62, P.113, L.114 No protein-ligand interaction detected (PLIP) SCN.11: 4 residues within 4Å: Chain A: R.117, W.118, Y.130 Ligands: EDO.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.118 SCN.12: 3 residues within 4Å: Chain A: E.100, Q.104, W.118 No protein-ligand interaction detected (PLIP) SCN.13: 4 residues within 4Å: Chain A: K.63, L.82, N.83, N.84 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.63 SCN.14: 6 residues within 4Å: Chain A: V.48, S.50, F.122, C.128, Y.134, S.135 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.50 SCN.15: 2 residues within 4Å: Chain A: T.165 Ligands: SCN.9 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Franco-Echevarria, E. et al., The structure of transcription termination factor Nrd1 reveals an original mode for GUAA recognition. Nucleic Acids Res. (2017)

Release Date

2017-08-02

Peptides

Protein NRD1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Protein NRD1

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