SMTL ID : 6rm9.1

Crystal structure of the DEAH-box ATPase Prp2 in complex with Spp2 and ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 17 residues within 4Å: Chain A: L.36, E.60, T.61, G.62, S.63, G.64, K.65, T.66, T.67, S.97, R.101, F.297, T.319, D.321, R.367 Ligands: MG.2, ACT.3 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:E.60, A:G.62, A:S.63, A:G.64, A:K.65, A:T.66, A:T.67, A:S.97, A:R.101, A:T.319, A:R.367, A:R.367 Water bridges: A:K.65, A:K.65, A:T.66, A:T.67, A:R.101, A:E.158, A:T.319 Salt bridges: A:K.65 pi-Stacking: A:F.297

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: T.66, D.157, E.158, S.317 Ligands: ADP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.66, H2O.2, H2O.2, H2O.4, H2O.5

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 6 residues within 4Å: Chain A: S.97, A.100, Q.293, A.294, F.297 Ligands: ADP.1 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.297 Water bridges: A:A.294 ACT.4: 7 residues within 4Å: Chain A: R.119, T.459, L.463, V.483, V.554, L.558 Ligands: GOL.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.459, A:L.463 Salt bridges: A:R.119

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: P.90, R.91, R.92, V.93, S.286, I.313 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.91, A:R.92, A:V.93, A:S.286 Water bridges: A:T.311, A:N.312 GOL.6: 3 residues within 4Å: Chain A: N.287, G.487 Ligands: ACT.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.287

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

PEG.7: 1 residues within 4Å: Chain B: E.9 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:K.430 Hydrogen bonds: B:E.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hamann, F. et al., Structural analysis of the intrinsically disordered splicing factor Spp2 and its binding to the DEAH-box ATPase Prp2. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-02-05

Peptides

Putative mRNA splicing factor: A
Putative pre-mRNA splicing protein: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Putative mRNA splicing factor

Putative pre-mRNA splicing protein

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