SMTL ID : 4tu8.1

STRUCTURE OF U2AF65 VARIANT WITH BRU5A6 DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

homo-dimer

Ligands

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

DU-DU-DU-DU-BRU-DA-DU.1: 33 residues within 4Å: Chain A: S.5, R.8, Y.10, 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: GOL.5, EDO.8, EDO.19 9 PLIP interactions: 1 interactions with chain B, 8 interactions with chain A Salt bridges: B:K.138, A:K.53 Hydrogen bonds: A:R.86, A:H.88 Water bridges: A:H.88, A:H.88, A:D.89 pi-Stacking: A:Y.10, A:H.88 DU-DU-DU-DU-BRU-DA-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 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.86, B:H.88 Water bridges: B:K.53, B:D.89 Salt bridges: B:K.53 pi-Stacking: B:Y.10, B:H.88

7 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: 4 residues within 4Å: Chain A: P.2, A.6, Y.90, Q.91 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.90, A:Q.91 DIO.13: 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.14: 2 residues within 4Å: Chain B: P.40, G.41 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.41 DIO.15: 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 DIO.16: 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:R.7, B:V.63 DIO.17: 3 residues within 4Å: Chain B: T.67, M.70, R.86 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.86

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: G.4, S.5, A.6, R.7, R.8 Ligands: DU-DU-DU-DU-BRU-DA-DU.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.3, A:S.5, A:A.6, A:R.7, A:R.8

9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 3 residues within 4Å: Chain A: K.114, L.123, F.126 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.114 EDO.7: 3 residues within 4Å: Chain A: S.62, V.63, D.64 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.63, A:D.64 Water bridges: A:S.62 EDO.8: 6 residues within 4Å: Chain A: R.8, A.46, Q.48, F.57, E.59 Ligands: DU-DU-DU-DU-BRU-DA-DU.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.59 EDO.9: 1 residues within 4Å: Chain A: A.29 No protein-ligand interaction detected (PLIP) EDO.10: 2 residues within 4Å: Chain A: P.2, P.94 No protein-ligand interaction detected (PLIP) EDO.19: 7 residues within 4Å: Chain A: H.88 Chain B: K.130, D.131, S.132, K.138 Ligands: DU-DU-DU-DU-BRU-DA-DU.1, DU-DU-DU-DU-BRU-DA-DU.1 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.130, B:S.132, B:K.138 EDO.20: 1 residues within 4Å: Chain B: D.165 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.165 EDO.21: 4 residues within 4Å: Chain B: L.116, M.161, L.163 Ligands: CPQ.18 No protein-ligand interaction detected (PLIP) EDO.22: 4 residues within 4Å: Chain B: A.156, G.157, N.159, M.161 No protein-ligand interaction detected (PLIP)

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

SO4.11: 2 residues within 4Å: Chain A: K.83, R.85 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.83 Salt bridges: A:K.83, A:R.85 SO4.12: 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 SO4.23: 2 residues within 4Å: Chain B: K.83, R.85 6 PLIP interactions: 6 interactions with chain B Water bridges: B:K.83, B:K.83, B:K.83, B:K.83 Salt bridges: B:K.83, B:R.85

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

CPQ.18: 7 residues within 4Å: Chain B: Y.107, Q.112, E.115, L.116, L.163, G.164 Ligands: EDO.21 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Q.112, B:L.116, B:L.163 Water bridges: 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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