SMTL ID : 5f9h.1

Crystal structure of RIG-I helicase-RD in complex with 24-mer 5' triphosphate hairpin RNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-hexamer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.580, C.583, C.634, C.639 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.580, A:C.583, A:C.634, A:C.639 ZN.6: 4 residues within 4Å: Chain C: C.580, C.583, C.634, C.639 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.580, C:C.583, C:C.634, C:C.639 ZN.8: 4 residues within 4Å: Chain E: C.580, C.583, C.634, C.639 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.580, E:C.583, E:C.634, E:C.639 ZN.11: 4 residues within 4Å: Chain G: C.580, C.583, C.634, C.639 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.580, G:C.583, G:C.634, G:C.639 ZN.15: 4 residues within 4Å: Chain I: C.580, C.583, C.634, C.639 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.580, I:C.583, I:C.634, I:C.639 ZN.18: 4 residues within 4Å: Chain K: C.580, C.583, C.634, C.639 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.580, K:C.583, K:C.634, K:C.639

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: F.55, P.56, Q.57, Q.59 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:P.56, A:Q.59 MG.3: 4 residues within 4Å: Chain A: Q.119, P.152 Chain B: A.2, U.3 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Chain A: K.40 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain E: N.146 Chain F: A.4 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain G: T.406, L.409 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.406 MG.13: 2 residues within 4Å: Chain G: N.111 Chain K: N.111 No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Chain E: N.111 Chain I: N.111 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain K: F.55, P.56, Q.59 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:P.56, K:Q.59

6 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.5: 12 residues within 4Å: Chain A: R.434, H.600, H.617, F.623, K.628, K.631, D.642, I.645, V.656, K.658 Chain B: A.1, C.23 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:H.600, A:K.628, A:D.642 Salt bridges: A:R.434, A:H.617, A:K.628, A:K.628, A:K.631, A:K.631, A:K.658 pi-Stacking: A:F.623, A:F.623 GTP.7: 11 residues within 4Å: Chain C: H.600, H.617, F.623, K.628, K.631, D.642, I.645, V.656, K.658 Chain D: A.1, C.23 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:H.600, C:K.628 Salt bridges: C:H.617, C:K.621, C:K.628, C:K.628, C:K.631, C:K.631, C:K.658 pi-Stacking: C:F.623, C:F.623 GTP.10: 12 residues within 4Å: Chain E: H.600, H.617, K.621, F.623, K.628, K.631, D.642, I.645, V.656, K.658 Chain F: A.1, C.23 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:H.600, E:K.621, E:K.628, E:D.642 Salt bridges: E:H.617, E:K.628, E:K.628, E:K.631, E:K.631, E:K.658 pi-Stacking: E:F.623, E:F.623 GTP.14: 11 residues within 4Å: Chain G: H.600, H.617, F.623, K.628, K.631, D.642, I.645, V.656, K.658 Chain H: A.1, C.23 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:H.600, G:K.621, G:K.628 Salt bridges: G:H.617, G:K.621, G:K.628, G:K.628, G:K.631, G:K.631, G:K.658 pi-Stacking: G:F.623, G:F.623 GTP.17: 11 residues within 4Å: Chain I: H.600, H.617, F.623, K.628, K.631, D.642, I.645, V.656, K.658 Chain J: A.1, C.23 10 PLIP interactions: 10 interactions with chain I Hydrogen bonds: I:H.600, I:K.628 Salt bridges: I:H.617, I:K.628, I:K.628, I:K.631, I:K.631, I:K.658 pi-Stacking: I:F.623, I:F.623 GTP.20: 11 residues within 4Å: Chain K: H.600, H.617, F.623, K.628, K.631, D.642, I.645, V.656, K.658 Chain L: A.1, C.23 10 PLIP interactions: 10 interactions with chain K Hydrogen bonds: K:H.600, K:K.628 Salt bridges: K:H.617, K:K.628, K:K.628, K:K.631, K:K.631, K:K.658 pi-Stacking: K:F.623, K:F.623

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Devarkar, S.C. et al., Structural basis for m7G recognition and 2'-O-methyl discrimination in capped RNAs by the innate immune receptor RIG-I. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-01-13

Peptides

Probable ATP-dependent RNA helicase DDX58: ACEGIK

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

I
I

K
K

Probable ATP-dependent RNA helicase DDX58

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