SMTL ID : 6zm2.1

Crystal structure of the DEAH-box ATPase Prp2 in complex with ADP-BeF3 and ssRNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x U- U- U- U- U- U- U- U: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3')(Non-covalent)

U-U-U-U-U-U-U-U.1: 33 residues within 4Å: Chain A: P.66, R.67, R.68, I.94, R.95, T.110, G.112, M.113, R.116, H.141, T.229, G.230, Q.231, Y.261, S.262, N.263, T.287, N.288, I.289, K.309, N.311, L.324, P.434, T.435, G.466, T.467, Q.533, H.592, P.593, S.594, T.615, S.616, Y.619 Protein-ligand interaction information (PLIP) not available

1 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.2: 9 residues within 4Å: Chain A: T.37, G.38, K.41, E.134, S.293, R.340, R.343 Ligands: ADP.3, MG.4 No protein-ligand interaction detected (PLIP)

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

ADP.3: 16 residues within 4Å: Chain A: L.12, E.36, T.37, G.38, S.39, G.40, K.41, T.42, T.43, R.77, T.295, R.343, V.344 Ligands: BEF.2, MG.4, HEZ.16 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:G.38, A:G.38, A:S.39, A:G.40, A:K.41, A:T.42, A:T.42, A:T.43, A:T.295, A:R.343 Water bridges: A:K.41, A:Q.44, A:T.295, A:R.343, A:R.343 Salt bridges: A:K.41, A:R.343, A:R.343 pi-Cation interactions: A:R.77, A:R.77

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: T.42, D.133, E.134 Ligands: BEF.2, ADP.3 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.42, H2O.1, H2O.1, H2O.3

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

PEG.5: 4 residues within 4Å: Chain A: L.408, N.409, Y.412, S.419 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.409 PEG.6: 4 residues within 4Å: Chain A: F.567, K.584, L.631 Ligands: MPO.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.584, A:L.631 PEG.7: 3 residues within 4Å: Chain A: N.502, E.506, R.531 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.506 Water bridges: A:N.502, A:Y.509 PEG.8: 5 residues within 4Å: Chain A: K.441, I.444, A.445, Q.448, A.564 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.413, A:K.441, A:Q.448

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 8 residues within 4Å: Chain A: E.36, T.37, A.166, T.167, R.188, N.335, M.338, G.339 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.36, A:T.37, A:T.37, A:R.188, A:N.335

2 x MPO: 3[N-MORPHOLINO]PROPANE SULFONIC ACID(Non-covalent)

MPO.10: 5 residues within 4Å: Chain A: Y.412, A.413, G.415, L.417 Ligands: PEG.6 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.412 MPO.11: 3 residues within 4Å: Chain A: T.120, S.121, D.126 No protein-ligand interaction detected (PLIP)

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

CL.12: 3 residues within 4Å: Chain A: N.335, R.351, Y.358 Ligand excluded by PLIP

3 x PGO: S-1,2-PROPANEDIOL(Non-covalent)

PGO.13: 4 residues within 4Å: Chain A: R.572, L.583, V.606, P.628 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.606, A:P.628 PGO.14: 11 residues within 4Å: Chain A: V.316, G.317, T.318, T.319, G.320, L.568, N.569, T.582, N.585, I.587, Y.609 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:T.582, A:I.587 Hydrogen bonds: A:T.318, A:T.318, A:T.319, A:T.319, A:G.320, A:N.569 Water bridges: A:A.570, A:Y.609, A:Y.609 PGO.15: 8 residues within 4Å: Chain A: V.465, R.483, D.493, T.496, L.497, S.594, V.596 Ligands: EDO.26 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.496, A:L.497 Hydrogen bonds: A:R.483, A:R.483, A:S.594

1 x HEZ: HEXANE-1,6-DIOL(Non-covalent)

HEZ.16: 5 residues within 4Å: Chain A: S.73, A.76, R.77, F.273 Ligands: ADP.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.76 Hydrogen bonds: A:D.80, A:D.80

9 x POL: N-PROPANOL(Non-covalent)

POL.17: 4 residues within 4Å: Chain A: A.52, G.53, Y.54, R.59 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.54 POL.18: 4 residues within 4Å: Chain A: V.300, P.346, G.347, K.348 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.346, A:K.348 POL.19: 5 residues within 4Å: Chain A: L.22, V.25, K.26, A.52, Y.54 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.26 Hydrogen bonds: A:Y.54 POL.20: 3 residues within 4Å: Chain A: G.577, Y.580, R.598 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.580 Hydrogen bonds: A:G.577 POL.21: 3 residues within 4Å: Chain A: L.423, R.425, R.428 No protein-ligand interaction detected (PLIP) POL.22: 6 residues within 4Å: Chain A: E.310, P.328, S.330, P.366, T.367, R.372 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.366 Hydrogen bonds: A:P.328, A:S.330 POL.23: 6 residues within 4Å: Chain A: N.263, M.264, P.265, T.467, R.522, R.526 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.467, A:R.522 POL.24: 4 residues within 4Å: Chain A: R.68, S.262, M.264, R.526 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.68 POL.25: 5 residues within 4Å: Chain A: G.306, Y.307, P.328, Y.353, E.361 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.328, A:P.328

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

EDO.26: 6 residues within 4Å: Chain A: V.465, D.493, S.595, R.621, S.622 Ligands: PGO.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.622 EDO.27: 6 residues within 4Å: Chain A: Q.29, V.30, K.150, T.153, F.177, D.178 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.153, A:D.178 EDO.28: 3 residues within 4Å: Chain A: G.87, D.98, T.100 No protein-ligand interaction detected (PLIP) EDO.29: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hamann, F. et al., The structure of Prp2 bound to RNA and ADP-BeF 3 - reveals structural features important for RNA unwinding by DEAH-box ATPases. Acta Crystallogr D Struct Biol (2021)

Release Date

2021-04-21

Peptides

Putative mRNA splicing factor: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Putative mRNA splicing factor