SMTL ID : 4oav.1

Complete human RNase L in complex with 2-5A (5'-ppp heptamer), AMPPCP and RNA substrate.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x PO4- PO4- A- A- A- A- PO4: RNA (5'-R(P*(PO4)P*(PO4)P*AP*AP*AP*AP*(PO4))-2')(Non-covalent)

PO4-PO4-A-A-A-A-PO4.1: 31 residues within 4Å: Chain A: M.286, R.289, R.290, Y.292, Y.334, R.335, F.344, R.407, H.409 Chain B: H.7, Q.14, E.35, E.36, E.37, G.38, W.40, N.45, Q.48, K.69, N.71, I.81, D.102, Y.104, F.106, E.111, V.114, Y.115, R.135, K.146, G.147, R.183 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.36 Salt bridges: B:H.7 PO4-PO4-A-A-A-A-PO4.2: 32 residues within 4Å: Chain A: H.7, Q.14, E.35, E.37, G.38, W.40, N.45, Q.48, K.69, N.71, I.81, D.102, Y.104, F.106, E.111, V.114, Y.115, R.135, K.146, G.147, R.183 Chain B: M.286, R.289, R.290, Y.292, E.307, I.333, Y.334, R.335, F.344, R.407, H.409 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.7

2 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.3: 20 residues within 4Å: Chain A: I.351, A.352, T.354, S.355, I.359, A.370, K.372, R.380, V.414, T.415, L.416, C.417, T.420, Q.469, N.470, L.472, D.483, D.485 Ligands: MG.4, MG.5 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.355, A:S.355, A:K.372, A:R.380, A:R.380, A:T.415, A:C.417, A:D.483 Water bridges: A:D.465, A:N.470, A:D.483 Salt bridges: A:K.372 ACP.6: 19 residues within 4Å: Chain B: I.351, A.352, T.354, S.355, I.359, A.370, K.372, R.380, V.414, T.415, C.417, T.420, Q.469, N.470, L.472, D.483, D.485 Ligands: MG.7, MG.8 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:S.355, B:S.355, B:K.372, B:R.380, B:R.380, B:T.415, B:C.417, B:D.483 Water bridges: B:D.465, B:Q.467, B:Q.467, B:Q.469, B:N.470, B:D.483, B:D.483 Salt bridges: B:K.372

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: N.470, D.483 Ligands: ACP.3, MG.5 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.483, H2O.1, H2O.1 MG.5: 6 residues within 4Å: Chain A: K.372, D.465, D.483, D.485 Ligands: ACP.3, MG.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.483, A:D.483, A:D.485, H2O.1, H2O.10 MG.7: 4 residues within 4Å: Chain B: N.470, D.483 Ligands: ACP.6, MG.8 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.483, H2O.19, H2O.33 MG.8: 6 residues within 4Å: Chain B: K.372, D.465, D.483, D.485 Ligands: ACP.6, MG.7 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.483, B:D.483, B:D.485, H2O.33, H2O.33

1 x PUP: (2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-4-hydroxy-2-({[(S)-hydroxy{[(2R,3S,4S)-4-hydroxy-2-(hydroxymethyl)tetrahydrofuran-3-yl]oxy}phosphoryl]oxy}methyl)tetrahydrofuran-3-yl dihydrogen phosphate(Non-covalent)

PUP.9: 10 residues within 4Å: Chain A: R.647 Chain B: K.586, T.587, M.624, F.627, Y.628, R.631, R.647, N.648, N.652 12 PLIP interactions: 1 interactions with chain A, 11 interactions with chain B Hydrogen bonds: A:R.647, B:Y.628, B:Y.628, B:R.631, B:R.647, B:N.652, B:N.652 Hydrophobic interactions: B:F.627, B:N.648 Water bridges: B:R.647, B:N.648 pi-Stacking: B:F.627

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Han, Y. et al., Structure of human RNase L reveals the basis for regulated RNA decay in the IFN response. Science (2014)

Release Date

2014-03-12

Peptides

PROTEIN (RNase L): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

PROTEIN (RNase L)

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