SMTL ID : 4o1p.2 (1 other biounit)

Crystal Structure of RNase L in complex with 2-5A and AMP-PNP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 20 residues within 4Å: Chain A: I.354, A.355, T.357, A.358, I.362, A.373, K.375, V.401, L.417, A.418, L.419, C.420, T.423, Q.471, N.472, L.474, D.485, D.487 Ligands: MG.2, MG.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.358, A:A.418, A:C.420, A:T.423, A:T.423 Salt bridges: A:K.375 ANP.5: 20 residues within 4Å: Chain B: I.354, A.355, T.357, A.358, I.362, A.373, K.375, R.383, L.417, A.418, L.419, C.420, T.423, Q.471, N.472, L.474, D.485, D.487 Ligands: MG.6, MG.7 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:D.356, B:A.358, B:K.375, B:R.383, B:R.383, B:A.418, B:C.420, B:T.423, B:T.423 Salt bridges: B:K.375

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.467, D.485, D.487 Ligands: ANP.1, MG.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.485, A:D.485, A:D.487, A:D.487, H2O.1 MG.3: 4 residues within 4Å: Chain A: N.472, D.485 Ligands: ANP.1, MG.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.485 MG.6: 5 residues within 4Å: Chain B: Q.471, N.472, D.485 Ligands: ANP.5, MG.7 No protein-ligand interaction detected (PLIP) MG.7: 5 residues within 4Å: Chain B: D.467, N.472, D.485 Ligands: ANP.5, MG.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.467, B:D.485

2 x 25L: [[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-3-hydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-3-hydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] phosphono hydrogen phosphate(Non-covalent)

25L.4: 22 residues within 4Å: Chain A: Q.17, E.38, W.41, W.43, S.48, Q.51, K.72, N.74, I.84, D.105, N.107, F.109, E.114, Y.118, R.138, K.149 Chain B: R.292, R.293, Y.295, R.338, F.347, S.411 29 PLIP interactions: 22 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:Q.17, A:W.43, A:Q.51, A:Q.51, A:N.74, A:E.114, A:Y.118, A:Y.118, B:S.411, B:S.411 Water bridges: A:N.74, A:N.107, A:N.107, A:R.138, A:G.150, A:G.150, A:R.186, B:R.292, B:R.338, B:R.338 Salt bridges: A:K.72, A:R.138, A:K.149, A:K.149, B:R.338 pi-Stacking: A:W.43, A:W.43, A:F.109 pi-Cation interactions: B:R.292 25L.8: 23 residues within 4Å: Chain A: R.292, R.293, Y.295, R.338, F.347, S.411 Chain B: Q.17, E.38, W.41, W.43, S.48, Q.51, K.72, N.74, I.84, D.105, N.107, F.109, E.114, V.117, Y.118, R.138, K.149 29 PLIP interactions: 21 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:Q.17, B:W.43, B:Q.51, B:Q.51, B:N.74, B:E.114, B:Y.118, A:Y.295, A:S.411, A:S.411 Water bridges: B:K.72, B:K.72, B:N.107, B:G.150, B:G.150, B:G.150, B:G.150, A:R.338, A:R.338, A:I.348 Salt bridges: B:K.72, B:R.138, B:K.149, B:K.149, A:R.338 pi-Stacking: B:W.43, B:W.43, B:F.109 pi-Cation interactions: A:R.292

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, H. et al., Dimeric structure of pseudokinase RNase L bound to 2-5A reveals a basis for interferon-induced antiviral activity. Mol.Cell (2014)

Release Date

2014-02-05

Peptides

Ribonuclease L: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Ribonuclease L

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