SMTL ID : 5jbg.1

Crystal structure of chicken LGP2 with 5'ppp 26-mer hairpin RNA with 3' GG overhang and ADP-AlF4-Mg2+ at 2.0 A resolution.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.560, C.563, C.616, C.619 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.560, A:C.563, A:C.616, A:C.619

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

ADP.2: 17 residues within 4Å: Chain A: S.7, E.8, L.9, H.10, Q.13, T.32, G.33, A.34, G.35, K.36, T.37, R.38, E.73, D.450, R.477 Ligands: ALF.3, MG.4 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:E.8, A:H.10, A:Q.13, A:G.33, A:A.34, A:G.35, A:K.36, A:T.37, A:T.37, A:R.38, A:R.38, A:E.73, A:D.450 Water bridges: A:S.7, A:T.37, A:T.37, A:T.37, A:R.38, A:Q.68, A:R.475 Salt bridges: A:K.36, A:R.477, A:R.477 pi-Cation interactions: A:R.38, A:R.38

1 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.3: 10 residues within 4Å: Chain A: T.32, G.33, K.36, E.138, A.174, G.448, R.475, R.477 Ligands: ADP.2, MG.4 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: T.37, E.138 Ligands: ADP.2, ALF.3 No protein-ligand interaction detected (PLIP)

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

SO4.5: 3 residues within 4Å: Chain A: H.10, G.11, Y.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.10, A:G.11, A:Y.12 SO4.6: 3 residues within 4Å: Chain A: S.545, R.548, Q.549 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.549 Salt bridges: A:R.548 SO4.7: 1 residues within 4Å: Chain A: K.650 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.650 SO4.8: 4 residues within 4Å: Chain A: F.279, C.280, R.281, K.282 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.281, A:K.282 Water bridges: A:T.283 SO4.9: 5 residues within 4Å: Chain A: K.62, H.141 Chain B: G.6, G.20, C.21 4 PLIP interactions: 4 interactions with chain A Water bridges: A:N.61, A:K.62, A:K.62 Salt bridges: A:K.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Uchikawa, E. et al., Structural Analysis of dsRNA Binding to Anti-viral Pattern Recognition Receptors LGP2 and MDA5. Mol.Cell (2016)

Release Date

2016-06-01

Peptides

LGP2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LGP2

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