SMTL ID : 6rm8.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-1-1-mer

Ligands

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

ADP.1: 16 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 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:G.62, A:S.63, A:G.64, A:K.65, A:T.66, A:T.66, A:T.67, A:S.97, A:D.321, A:R.367, A:R.367 Water bridges: A:T.61, A:K.65, A:T.66, A:R.101, A:E.158, A:T.316 Salt bridges: A:K.65

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.1, H2O.2, H2O.2, H2O.4

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

SO4.3: 6 residues within 4Å: Chain A: G.254, Q.255, Y.285, S.286, T.311, K.333 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.255, A:S.286 Water bridges: A:Q.255, A:S.286 Salt bridges: A:K.333 SO4.4: 3 residues within 4Å: Chain A: G.490, R.507, S.618 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.490, A:S.618 Water bridges: A:R.507, A:S.618 Salt bridges: A:R.507 SO4.5: 2 residues within 4Å: Chain A: R.109, H.112 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.109 Water bridges: A:R.109 Salt bridges: A:H.112 SO4.6: 5 residues within 4Å: Chain A: R.92, M.96, F.120, E.121, R.550 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.550, A:R.550, A:R.550 Salt bridges: A:R.92, A:R.550 SO4.7: 4 residues within 4Å: Chain A: R.507, D.517, T.520, S.618 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.517, A:S.618 Water bridges: A:R.507, A:R.507, A:S.618 Salt bridges: A:R.507 SO4.8: 2 residues within 4Å: Chain A: T.448, R.449 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.449 Water bridges: A:V.450 Salt bridges: A:R.449 SO4.9: 3 residues within 4Å: Chain A: N.598, R.599, R.605 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.598, A:R.599 Salt bridges: A:R.599, A:R.605 SO4.10: 2 residues within 4Å: Chain A: R.605, T.612 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.605 SO4.11: 5 residues within 4Å: Chain A: R.119, N.287, E.488, R.550, V.554 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.287, A:E.488 Water bridges: A:G.487, A:R.550 Salt bridges: A:R.119, A:R.550

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.12: 4 residues within 4Å: Chain A: P.90, R.91, R.92 Ligands: CL.13 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain A: R.91, S.286, I.313 Ligands: CL.12 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain A: G.410, D.412, D.413 Ligand excluded by PLIP

1 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.15: 5 residues within 4Å: Chain A: T.471, Q.472, G.474, D.567, A.571 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.474, A:D.567, A:D.567 Water bridges: A:G.474

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

PEG.16: 8 residues within 4Å: Chain A: I.118, R.119, T.134, G.136, M.137, R.140, H.165, P.458 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.119, A:T.134 Water bridges: A:G.136, A:R.140, A:H.165, A:Q.405, A:Q.405

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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