SMTL ID : 4tu7.1

Structure of U2AF65 D231V variant with BrU5 DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-dimer

Ligands

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

DU-DU-DU-DU-BRU-DU-DU.1: 32 residues within 4Å: Chain A: R.8, Y.10, G.12, Q.48, K.53, N.54, F.55, F.57, K.83, R.85, R.86, P.87, H.88, V.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 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.86, A:H.88 Water bridges: A:K.53, B:K.130, B:K.138 Salt bridges: A:K.53, B:K.138 pi-Stacking: A:Y.10 DU-DU-DU-DU-BRU-DU-DU.2: 15 residues within 4Å: Chain B: R.8, Y.10, G.12, Q.48, K.53, N.54, F.55, F.57, E.59, K.83, R.85, R.86, P.87, H.88, V.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

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

DIO.3: 2 residues within 4Å: Chain A: Y.107, N.109 No protein-ligand interaction detected (PLIP) DIO.4: 6 residues within 4Å: Chain A: P.2, L.3, A.6, Y.90, Q.91, P.92 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.90 DIO.11: 5 residues within 4Å: Chain B: K.114, L.123, K.124, A.125, F.126 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.114 Water bridges: 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

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

SO4.5: 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:D.147 Salt bridges: A:K.83, A:R.85 SO4.6: 4 residues within 4Å: Chain A: R.7, R.8, E.59 Ligands: DU-DU-DU-DU-BRU-DU-DU.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.59 Salt bridges: A:R.7, A:R.8 SO4.7: 2 residues within 4Å: Chain A: M.70, R.86 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.86 SO4.14: 4 residues within 4Å: Chain B: R.7, S.62, V.63, D.64 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.63, B:D.64 SO4.15: 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 SO4.16: 2 residues within 4Å: Chain B: M.70, R.86 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.86

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 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.9: 1 residues within 4Å: Chain A: R.32 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.32 GOL.10: 5 residues within 4Å: Chain A: K.114, L.123, K.124, A.125, F.126 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.123 Water bridges: A:F.126 GOL.17: 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.13: 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