SMTL ID : 3vaj.1

Structure of U2AF65 variant with BrU5C6 DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

DU-DU-DU-DU-BRU-DC-DU.1: 32 residues within 4Å: Chain A: S.5, 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 Chain B: K.98, F.100, G.102, G.103, N.127, V.129, K.130, S.132, K.138, Y.140, F.142, K.166, K.167, L.169, Q.171, R.172, A.173 Ligands: SO4.6 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.86, A:H.88 Water bridges: A:H.88, A:H.88, B:S.132, B:K.138 Salt bridges: A:K.53, B:K.138 pi-Stacking: A:Y.10, A:H.88 DU-DU-DU-DU-BRU-DC-DU.2: 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:R.86, B:H.88 Water bridges: B:K.53 Salt bridges: B:K.53 pi-Stacking: B:Y.10, B:H.88

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

DIO.3: 8 residues within 4Å: Chain A: N.106, Y.107, L.108, N.109, K.130, 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.90 Water bridges: A:Q.91 DIO.9: 4 residues within 4Å: Chain B: L.123, K.124, A.125, F.126 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.126 Water bridges: B:K.114 DIO.10: 2 residues within 4Å: Chain B: P.40, G.41 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.41 DIO.11: 8 residues within 4Å: Chain B: N.106, Y.107, L.108, N.109, K.130, G.135, L.136, S.137 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.137 Water bridges: B:D.110

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

SO4.5: 2 residues within 4Å: Chain A: K.83, R.85 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.83, A:R.85 Salt bridges: A:K.83, A:R.85 SO4.6: 4 residues within 4Å: Chain A: G.4, S.5, R.8 Ligands: DU-DU-DU-DU-BRU-DC-DU.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.5, A:A.6 Water bridges: A:L.3 Salt bridges: A:R.8 SO4.7: 3 residues within 4Å: Chain A: M.70, R.86, I.148 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.86 SO4.13: 3 residues within 4Å: Chain B: R.7, S.62, V.63 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.63 Water bridges: B:Q.38, B:Q.38 Salt bridges: B:R.7 SO4.14: 2 residues within 4Å: Chain B: K.83, R.85 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.83, B:K.83 Salt bridges: B:K.83, B:R.85 SO4.15: 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

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 4 residues within 4Å: Chain A: I.49, N.50, Q.51, D.52 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.50, A:Q.51 GOL.16: 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.12: 6 residues within 4Å: Chain B: Y.107, L.108, Q.112, E.115, L.163, G.164 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.108, B:Q.112, B:L.163 Hydrogen bonds: B:E.115

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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