SMTL ID : 3vak.1

Structure of U2AF65 variant with BrU5 DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 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: 17 residues within 4Å: Chain A: K.98, F.100, G.102, G.103, N.127, V.129, K.130, S.132, S.137, K.138, Y.140, F.142, K.166, L.169, Q.171, R.172, A.173 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.140 Water bridges: A:K.138, A:K.138, A:K.138 Salt bridges: A:K.138 DU-DU-DU-DU-BRU-DU-DU.2: 32 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.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, SO4.7 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:R.86, A:H.88 Salt bridges: A:K.53, B:K.138 pi-Stacking: A:Y.10 Water bridges: B:S.132, B:K.138, B:K.138, B:K.138

5 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.137 Water bridges: A:N.109 DIO.4: 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:Q.91 DIO.12: 5 residues within 4Å: Chain B: K.114, L.123, K.124, A.125, F.126 No protein-ligand interaction detected (PLIP) DIO.13: 2 residues within 4Å: Chain B: P.40, G.41 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.41 DIO.14: 5 residues within 4Å: Chain B: N.106, Y.107, 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)

SO4.5: 2 residues within 4Å: Chain A: K.83, R.85 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.83, A:R.85 SO4.6: 4 residues within 4Å: Chain A: Q.48, I.49, N.50 Ligands: DU-DU-DU-DU-BRU-DU-DU.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.48, A:N.50 SO4.7: 4 residues within 4Å: Chain A: R.7, R.8, E.59 Ligands: DU-DU-DU-DU-BRU-DU-DU.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.59 Water bridges: A:S.5, A:R.7 Salt bridges: A:R.7, A:R.8 SO4.8: 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 SO4.16: 4 residues within 4Å: Chain B: R.7, R.61, S.62, V.63 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.63 Water bridges: B:Q.38 Salt bridges: B:R.7 SO4.17: 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 SO4.18: 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

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 3 residues within 4Å: Chain A: 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.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.11: 5 residues within 4Å: Chain A: K.114, L.123, K.124, A.125, F.126 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.114, A:L.123, A:F.126 Water bridges: A:K.114 GOL.19: 2 residues within 4Å: Chain B: I.155, 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.15: 4 residues within 4Å: Chain B: Y.107, Q.112, E.115, L.163 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.112, B:L.163

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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