SMTL ID : 3val.1

Structure of U2AF65 variant with BrU5C1 DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

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

DU-DU-DU-BRU-DU-DU.1: 13 residues within 4Å: Chain D: K.98, F.100, N.127, V.129, S.132, K.138, G.139, Y.140, F.142, L.169, Q.171, R.172, A.173 3 PLIP interactions: 3 interactions with chain D Water bridges: D:K.138, D:K.138 Salt bridges: D:K.138 DU-DU-DU-BRU-DU-DU.2: 13 residues within 4Å: Chain A: K.98, F.100, G.103, N.127, V.129, S.132, K.138, Y.140, F.142, L.169, Q.171, R.172, A.173 5 PLIP interactions: 5 interactions with chain A Water bridges: A:S.132, A:K.138, A:K.138, A:K.138 Salt bridges: A:K.138 DU-DU-DU-BRU-DU-DU.3: 28 residues within 4Å: Chain C: K.98, F.100, G.103, N.127, V.129, S.132, K.138, Y.140, F.142, K.166, L.169, Q.171, R.172, A.173 Chain D: 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, D.89 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:R.86, D:H.88 Salt bridges: D:K.53, C:K.138 pi-Stacking: D:Y.10, D:H.88 Water bridges: C:K.138, C:K.138 DU-DU-DU-BRU-DU-DU.4: 27 residues within 4Å: Chain A: S.5, 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, D.89 Chain B: K.98, F.100, N.127, V.129, K.130, S.132, K.138, Y.140, F.142, Q.171, R.172, A.173 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:R.86, A:H.88, B:S.132 Water bridges: A:H.88, A:H.88, B:S.132, B:S.132 Salt bridges: A:K.53, B:K.138 pi-Stacking: A:Y.10, A:H.88

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

DIO.5: 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:Q.91 DIO.8: 3 residues within 4Å: Chain B: R.32, P.40, G.41 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.41 Water bridges: B:R.32 DIO.11: 6 residues within 4Å: Chain C: P.2, L.3, A.6, Y.90, Q.91, L.93 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.90 DIO.15: 3 residues within 4Å: Chain D: R.32, P.40, G.41 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.41

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

SO4.6: 3 residues within 4Å: Chain A: K.83, R.85, D.147 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.85 Salt bridges: A:K.83, A:R.85 SO4.7: 4 residues within 4Å: Chain A: T.67, M.70, R.86, Y.90 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.90 Salt bridges: A:R.86 SO4.9: 3 residues within 4Å: Chain B: M.70, R.86, Y.90 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.90, B:Y.90 Water bridges: B:R.86 Salt bridges: B:R.86 SO4.10: 2 residues within 4Å: Chain B: S.62, V.63 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.63 SO4.12: 2 residues within 4Å: Chain C: K.83, R.85 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:K.83, C:R.85 SO4.13: 3 residues within 4Å: Chain C: R.7, R.8, E.59 4 PLIP interactions: 4 interactions with chain C Water bridges: C:R.7, C:R.7 Salt bridges: C:R.7, C:R.8 SO4.14: 4 residues within 4Å: Chain C: T.67, M.70, R.86, I.148 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.86 SO4.16: 4 residues within 4Å: Chain D: R.7, R.61, S.62, V.63 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:V.63 SO4.17: 3 residues within 4Å: Chain D: M.70, R.86, Y.90 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.86 SO4.18: 2 residues within 4Å: Chain D: K.83, R.85 3 PLIP interactions: 3 interactions with chain D Water bridges: D:K.83 Salt bridges: D:K.83, D:R.85 SO4.19: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
I

Splicing factor U2AF 65 kDa subunit

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