SMTL ID : 6xlw.1

Crystal structure of U2AF65 bound to AdML splice site sequence

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x U- U- DU- U- U- BRU- C- C: DNA/RNA (5'-R(P*UP*UP*(UD)P*UP*U)-D(P*(BRU))-R(P*CP*C)-3')(Non-covalent)

U-U-DU-U-U-BRU-C-C.1: 43 residues within 4Å: Chain A: R.9, R.13, Y.15, N.18, N.55, K.58, N.59, F.60, F.62, K.88, R.90, R.91, P.92, H.93, D.94, T.115, V.116, V.117, D.119, K.123, F.125, G.127, G.128, N.152, V.154, K.155, S.157, K.163, Y.165, F.167, K.191, K.192, L.193, L.194, Q.196, R.197, A.198, V.200, G.201, A.202, K.203 Ligands: NA.6, NA.7 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.91, A:H.93 Water bridges: A:R.90, A:D.94 pi-Stacking: A:Y.15, A:H.93

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: M.75, I.89, R.90, V.116 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.90

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 3 residues within 4Å: Chain A: D.136, Q.137, E.140 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.136, A:Q.137

4 x NA: SODIUM ION(Non-functional Binders)

NA.4: 1 residues within 4Å: Chain A: S.157 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.157 NA.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.6: 6 residues within 4Å: Chain A: N.18, N.59, Q.85, K.155, G.160 Ligands: U-U-DU-U-U-BRU-C-C.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.18, A:N.59 Water bridges: A:Q.85 NA.7: 5 residues within 4Å: Chain A: K.58, N.59, S.157, A.158 Ligands: U-U-DU-U-U-BRU-C-C.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maji, D. et al., Representative cancer-associated U2AF2 mutations alter RNA interactions and splicing. J.Biol.Chem. (2020)

Release Date

2020-10-07

Peptides

Splicing factor U2AF 65 kDa subunit: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Splicing factor U2AF 65 kDa subunit

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