SMTL ID : 3vah.1

Structure of U2AF65 variant with BrU3C4 DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

DU-DU-BRU-DC-DU.1: 13 residues within 4Å: Chain B: R.8, Y.10, G.12, K.53, N.54, F.55, F.57, K.83, R.85, R.86, P.87, H.88, D.89 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.10, B:K.53 Water bridges: B:N.13, B:D.52, B:N.54 Salt bridges: B:K.83 DU-DU-BRU-DC-DU.2: 31 residues within 4Å: Chain A: R.8, Y.10, N.13, Q.48, I.49, N.50, 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.102, G.103, N.127, V.129, K.130, S.132, K.138, G.139, Y.140, F.142, L.169, Q.171, A.173 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Y.10, A:K.53, B:K.98, B:N.127 Water bridges: A:N.54, A:K.83, B:K.98 Salt bridges: A:K.83 Halogen bonds: A:N.13 pi-Stacking: B:F.142

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

DIO.3: 5 residues within 4Å: Chain A: P.2, L.3, A.6, Y.90, Q.91 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.90 DIO.6: 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:K.114 DIO.7: 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.8: 6 residues within 4Å: Chain B: N.106, Y.107, N.109, G.135, L.136, S.137 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.137

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

SO4.4: 2 residues within 4Å: Chain A: K.83, R.85 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.85 Salt bridges: A:K.83, A:R.85 SO4.5: 3 residues within 4Å: Chain A: G.4, S.5, A.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.5, A:S.5, A:A.6 SO4.10: 4 residues within 4Å: Chain B: R.7, R.61, S.62, V.63 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.63 Salt bridges: B:R.7 SO4.11: 2 residues within 4Å: Chain B: K.83, R.85 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.83, B:R.85 SO4.12: 3 residues within 4Å: Chain B: M.70, R.86, Y.90 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.86

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

CPQ.9: 5 residues within 4Å: Chain B: Y.107, Q.112, L.116, L.163, G.164 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Q.112, B:L.116, B:L.163 Hydrogen bonds: B:G.164

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 2 residues within 4Å: Chain B: 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

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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