SMTL ID : 3vag.1

Structure of U2AF65 variant with BrU3C2 DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

homo-dimer

Ligands

2 x DC- BRU- DU- DU- DU- DU: DNA 5'-D(*U*CP*(BRU)P*UP*UP*UP*U)-3'(Non-covalent)

DC-BRU-DU-DU-DU-DU.1: 30 residues within 4Å: Chain A: R.8, Y.10, Q.48, K.53, N.54, F.55, F.57, K.83, R.85, R.86, P.87, H.88, D.89 Chain B: K.98, F.100, G.103, N.127, V.129, K.130, S.132, K.138, G.139, Y.140, F.142, L.169, Q.171, R.172, A.173 Ligands: SO4.7, SO4.8 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.171, B:A.173 pi-Stacking: B:F.100 Water bridges: A:N.13, A:K.83 DC-BRU-DU-DU-DU-DU.2: 14 residues within 4Å: Chain B: R.8, Y.10, G.12, K.53, N.54, F.55, F.57, E.59, K.83, R.85, R.86, P.87, H.88, D.89 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.10, B:K.53, B:N.54 Water bridges: B:N.13 Salt bridges: B:K.83

6 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)

DIO.3: 7 residues within 4Å: Chain A: N.106, Y.107, L.108, N.109, G.135, L.136, S.137 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.137 DIO.4: 5 residues within 4Å: Chain A: P.2, L.3, A.6, Y.90, Q.91 No protein-ligand interaction detected (PLIP) DIO.5: 5 residues within 4Å: Chain A: Q.38, A.39, R.61, S.62, E.65 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.38, A:S.62 DIO.11: 5 residues within 4Å: Chain B: K.114, L.123, K.124, A.125, F.126 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.126 DIO.12: 3 residues within 4Å: Chain B: R.32, P.40, G.41 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.41 DIO.13: 7 residues within 4Å: Chain B: N.106, Y.107, L.108, K.130, G.135, L.136, S.137 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.137

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

SO4.6: 2 residues within 4Å: Chain A: K.83, R.85 6 PLIP interactions: 6 interactions with chain A Water bridges: A:K.83, A:K.83, A:K.83, A:K.83 Salt bridges: A:K.83, A:R.85 SO4.7: 5 residues within 4Å: Chain A: Q.48, I.49, N.50 Ligands: DC-BRU-DU-DU-DU-DU.1, DC-BRU-DU-DU-DU-DU.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.48 Water bridges: A:N.50 SO4.8: 4 residues within 4Å: Chain A: R.7, R.8, E.59 Ligands: DC-BRU-DU-DU-DU-DU.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.59 Water bridges: A:S.5 Salt bridges: A:R.7, A:R.8 SO4.9: 3 residues within 4Å: Chain A: R.86, Y.90, I.148 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.90 Salt bridges: A:R.86 SO4.15: 3 residues within 4Å: Chain B: R.7, S.62, V.63 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.7, B:V.63 SO4.16: 2 residues within 4Å: Chain B: K.83, R.85 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.83 Salt bridges: B:K.83, B:R.85 SO4.17: 2 residues within 4Å: Chain B: R.86, Y.90 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.86

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 4 residues within 4Å: Chain A: I.49, N.50, Q.51, D.52 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.50, A:Q.51, A:D.52 GOL.18: 3 residues within 4Å: Chain B: I.155, Q.171, R.172 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.172, B:R.172 Water bridges: B:V.170

1 x CPQ: N,N-BIS(3-D-GLUCONAMIDOPROPYL)DEOXYCHOLAMIDE(Non-covalent)

CPQ.14: 3 residues within 4Å: Chain B: Y.107, Q.112, G.164 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Q.112

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jenkins, J.L. et al., U2AF65 adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifs. Nucleic Acids Res. (2013)

Release Date

2013-02-13

Peptides

Splicing factor U2AF 65 kDa subunit: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Splicing factor U2AF 65 kDa subunit

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