SMTL ID : 1nu4.6 (6 other biounits)

U1A RNA binding domain at 1.8 angstrom resolution reveals a pre-organized C-terminal helix

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 1 residues within 4Å: Chain A: R.69 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:R.69, H2O.1 MG.2: 3 residues within 4Å: Chain A: D.41 Chain B: D.41 Ligands: MG.10 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:D.41, A:D.41, H2O.2, H2O.4, H2O.4 MG.9: 1 residues within 4Å: Chain B: R.69 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:R.69, H2O.3 MG.10: 3 residues within 4Å: Chain A: D.41 Chain B: D.41 Ligands: MG.2 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:D.41, A:D.41, H2O.2, H2O.2, H2O.4

12 x MLA: MALONIC ACID(Non-covalent)

MLA.3: 4 residues within 4Å: Chain A: Y.12, F.55, A.86, K.87 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.12, A:F.55 Hydrogen bonds: A:K.87 Water bridges: A:Y.12, A:T.88 Salt bridges: A:K.87 MLA.4: 3 residues within 4Å: Chain A: V.61, S.62, T.65 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.65 Hydrogen bonds: A:T.65 Water bridges: A:R.69 MLA.5: 2 residues within 4Å: Chain A: R.6, Y.85 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.85 Water bridges: A:R.69, A:R.69 Salt bridges: A:R.6 MLA.6: 6 residues within 4Å: Chain A: K.26, H.30, I.39, L.40, D.41, I.42 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A Salt bridges: B:K.22, B:K.26, B:K.26, A:K.26, A:H.30, A:H.30 Hydrogen bonds: A:I.39 Water bridges: A:K.26, A:Q.38 MLA.7: 2 residues within 4Å: Chain A: A.94 Chain B: R.51 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.94, A:A.94 Salt bridges: B:R.51 MLA.8: 7 residues within 4Å: Chain A: K.22, S.45, R.46, S.47 Chain B: L.40, K.59, M.96 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.45, A:R.46, A:S.47 Salt bridges: A:K.22, B:K.59 Hydrophobic interactions: B:L.40, B:K.59 MLA.11: 4 residues within 4Å: Chain B: Y.12, F.55, A.86, K.87 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.12, B:F.55 Hydrogen bonds: B:K.87 Water bridges: B:T.88 Salt bridges: B:K.87 MLA.12: 3 residues within 4Å: Chain B: V.61, S.62, T.65 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.65 Water bridges: B:R.69 MLA.13: 2 residues within 4Å: Chain B: R.6, Y.85 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.85 Water bridges: B:R.69, B:R.69 Salt bridges: B:R.6 MLA.14: 6 residues within 4Å: Chain B: K.26, H.30, I.39, L.40, D.41, I.42 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:I.39 Water bridges: B:K.26, B:Q.38 Salt bridges: B:K.26, B:H.30, B:H.30, A:K.22, A:K.26, A:K.26 MLA.15: 2 residues within 4Å: Chain A: R.51 Chain B: A.94 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.94, B:A.94 Salt bridges: A:R.51 MLA.16: 7 residues within 4Å: Chain A: L.40, K.59, M.96 Chain B: K.22, S.45, R.46, S.47 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.45, B:R.46, B:S.47 Salt bridges: B:K.22, A:K.59 Hydrophobic interactions: A:L.40, A:K.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rupert, P.B. et al., U1A RNA-binding domain at 1.8 A resolution. Acta Crystallogr.,Sect.D (2003)

Release Date

2003-02-14

Peptides

U1A RNA binding domain: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

U1A RNA binding domain

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