SMTL ID : 4tu9.1

STRUCTURE OF U2AF65 VARIANT WITH BRU5G6 DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-dimer

Ligands

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

DU-DU-DU-DU-BRU-DG.1: 31 residues within 4Å: Chain A: 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, G.139, Y.140, F.142, K.166, K.167, L.169, Q.171, R.172, A.173 9 PLIP interactions: 2 interactions with chain B, 7 interactions with chain A Water bridges: B:K.138, A:H.88, A:H.88 Salt bridges: B:K.138, A:K.53 Hydrogen bonds: A:R.86, A:H.88 pi-Stacking: A:Y.10, A:H.88 DU-DU-DU-DU-BRU-DG.2: 11 residues within 4Å: Chain B: Y.10, G.12, K.53, N.54, F.55, F.57, K.83, R.85, R.86, P.87, H.88 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.86, B:H.88 Water bridges: B:K.53, B:H.88 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.137 Water bridges: A:D.110 DIO.4: 4 residues within 4Å: Chain A: P.2, A.6, Y.90, Q.91 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.91 DIO.5: 5 residues within 4Å: Chain A: K.114, L.123, K.124, A.125, F.126 No protein-ligand interaction detected (PLIP) DIO.10: 4 residues within 4Å: Chain B: K.114, L.123, K.124, F.126 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.114 Water bridges: B:F.126 DIO.11: 7 residues within 4Å: Chain B: N.106, Y.107, L.108, N.109, G.135, L.136, S.137 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.137

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

SO4.6: 2 residues within 4Å: Chain A: K.83, R.85 7 PLIP interactions: 7 interactions with chain A Water bridges: A:K.83, A:K.83, A:K.83, A:K.83, A:R.85 Salt bridges: A:K.83, A:R.85 SO4.7: 3 residues within 4Å: Chain A: G.4, S.5, R.8 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.5 Water bridges: A:A.6, A:R.8, A:R.8 Salt bridges: A:R.8 SO4.8: 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: 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 SO4.14: 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 SO4.15: 2 residues within 4Å: Chain B: M.70, R.86 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.86

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 4 residues within 4Å: Chain A: I.49, N.50, Q.51, D.52 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.51, A:D.52, A:D.52 Water bridges: A:N.50 GOL.16: 5 residues within 4Å: Chain B: Q.48, I.49, N.50, F.55, F.57 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.48, B:I.49

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

CPQ.12: 5 residues within 4Å: Chain B: Y.107, Q.112, E.115, L.163, G.164 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Q.112, B:L.163 Hydrogen bonds: B:G.164

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Agrawal, A.A. et al., Structure-guided U2AF65 variant improves recognition and splicing of a defective pre-mRNA. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-11-26

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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