SMTL ID : 5udj.2 (1 other biounit)

IFIT1 monomeric mutant (L457E/L464E) with Gppp-AAAA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-tetramer

Ligands

4 x G3A- A- A- A: RNA (5'-D(*(G3A))-R(P*AP*AP*A)-3')(Non-covalent)

G3A-A-A-A.1: 44 residues within 4Å: Chain A: R.39, Q.43, L.47, T.49, W.148, L.151, K.152, G.154, G.155, K.156, Y.158, I.184, Y.187, R.188, G.191, F.192, L.194, A.195, N.217, Y.219, Y.253, R.256, Y.257, K.260, R.263, V.286, L.287, H.290, Q.291, L.294, K.297, K.337, F.340, E.341, V.342, L.345, D.346, R.349, V.373, V.374, T.377, D.380, H.384, L.414 41 PLIP interactions: 41 interactions with chain A Hydrogen bonds: A:L.151, A:G.155, A:Y.158, A:Y.158, A:R.188, A:R.188, A:N.217, A:Y.219 Water bridges: A:R.39, A:R.39, A:Q.43, A:Q.43, A:Q.43, A:W.148, A:K.152, A:K.152, A:K.156, A:E.177, A:R.256, A:R.256, A:R.256, A:R.256, A:K.337, A:K.337, A:K.337, A:E.341, A:V.373, A:V.373, A:V.374 Salt bridges: A:R.39, A:R.39, A:K.152, A:K.152, A:R.188, A:R.188, A:R.188, A:R.256, A:K.337 pi-Stacking: A:Y.219 pi-Cation interactions: A:W.148, A:W.148 G3A-A-A-A.5: 44 residues within 4Å: Chain B: R.39, Q.43, L.47, T.49, W.148, L.151, K.152, G.154, G.155, K.156, Y.158, I.184, Y.187, R.188, G.191, F.192, L.194, A.195, N.217, Y.219, Y.253, R.256, Y.257, K.260, R.263, V.286, L.287, H.290, Q.291, L.294, K.297, K.337, F.340, E.341, V.342, L.345, D.346, R.349, V.373, V.374, T.377, D.380, H.384, L.414 41 PLIP interactions: 41 interactions with chain B Hydrogen bonds: B:L.151, B:G.155, B:Y.158, B:Y.158, B:R.188, B:R.188, B:N.217, B:Y.219 Water bridges: B:R.39, B:R.39, B:Q.43, B:Q.43, B:Q.43, B:W.148, B:K.152, B:K.152, B:K.156, B:E.177, B:R.256, B:R.256, B:R.256, B:R.256, B:K.337, B:K.337, B:K.337, B:E.341, B:V.373, B:V.373, B:V.374 Salt bridges: B:R.39, B:R.39, B:K.152, B:K.152, B:R.188, B:R.188, B:R.188, B:R.256, B:K.337 pi-Stacking: B:Y.219 pi-Cation interactions: B:W.148, B:W.148 G3A-A-A-A.9: 44 residues within 4Å: Chain C: R.39, Q.43, L.47, T.49, W.148, L.151, K.152, G.154, G.155, K.156, Y.158, I.184, Y.187, R.188, G.191, F.192, L.194, A.195, N.217, Y.219, Y.253, R.256, Y.257, K.260, R.263, V.286, L.287, H.290, Q.291, L.294, K.297, K.337, F.340, E.341, V.342, L.345, D.346, R.349, V.373, V.374, T.377, D.380, H.384, L.414 41 PLIP interactions: 41 interactions with chain C Hydrogen bonds: C:L.151, C:G.155, C:Y.158, C:Y.158, C:R.188, C:R.188, C:N.217, C:Y.219 Water bridges: C:E.32, C:R.39, C:R.39, C:Q.43, C:Q.43, C:Q.43, C:W.148, C:K.152, C:K.152, C:K.156, C:E.177, C:R.256, C:R.256, C:R.256, C:R.256, C:K.337, C:K.337, C:E.341, C:V.373, C:V.373, C:V.374 Salt bridges: C:R.39, C:R.39, C:K.152, C:K.152, C:R.188, C:R.188, C:R.188, C:R.256, C:K.337 pi-Stacking: C:Y.219 pi-Cation interactions: C:W.148, C:W.148 G3A-A-A-A.13: 44 residues within 4Å: Chain D: R.39, Q.43, L.47, T.49, W.148, L.151, K.152, G.154, G.155, K.156, Y.158, I.184, Y.187, R.188, G.191, F.192, L.194, A.195, N.217, Y.219, Y.253, R.256, Y.257, K.260, R.263, V.286, L.287, H.290, Q.291, L.294, K.297, K.337, F.340, E.341, V.342, L.345, D.346, R.349, V.373, V.374, T.377, D.380, H.384, L.414 41 PLIP interactions: 41 interactions with chain D Hydrogen bonds: D:L.151, D:G.155, D:Y.158, D:Y.158, D:R.188, D:R.188, D:N.217, D:Y.219 Water bridges: D:E.32, D:R.39, D:R.39, D:Q.43, D:Q.43, D:Q.43, D:W.148, D:K.152, D:K.152, D:K.156, D:E.177, D:R.256, D:R.256, D:R.256, D:R.256, D:K.337, D:K.337, D:E.341, D:V.373, D:V.373, D:V.374 Salt bridges: D:R.39, D:R.39, D:K.152, D:K.152, D:R.188, D:R.188, D:R.188, D:R.256, D:K.337 pi-Stacking: D:Y.219 pi-Cation interactions: D:W.148, D:W.148

4 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 6 residues within 4Å: Chain A: H.64, L.65, H.108 Chain B: L.404, L.443, F.446 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.64, A:G.67 PGE.6: 6 residues within 4Å: Chain A: L.404, L.443, F.446 Chain B: H.64, L.65, H.108 2 PLIP interactions: 2 interactions with chain B Water bridges: B:H.64, B:G.67 PGE.10: 6 residues within 4Å: Chain C: H.64, L.65, H.108 Chain D: L.404, L.443, F.446 2 PLIP interactions: 2 interactions with chain C Water bridges: C:H.64, C:G.67 PGE.14: 6 residues within 4Å: Chain C: L.404, L.443, F.446 Chain D: H.64, L.65, H.108 2 PLIP interactions: 2 interactions with chain D Water bridges: D:H.64, D:G.67

8 x CA: CALCIUM ION(Non-covalent)

CA.3: 2 residues within 4Å: Chain A: D.48, S.250 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.48, A:D.48, H2O.8, H2O.10 CA.4: 1 residues within 4Å: Chain A: E.78 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.78, A:E.78, H2O.12 CA.7: 2 residues within 4Å: Chain B: D.48, S.250 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.48, B:D.48, H2O.22, H2O.24 CA.8: 1 residues within 4Å: Chain B: E.78 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.78, B:E.78, H2O.27 CA.11: 2 residues within 4Å: Chain C: D.48, S.250 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.48, C:D.48, H2O.37, H2O.39 CA.12: 1 residues within 4Å: Chain C: E.78 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.78, C:E.78, H2O.41 CA.15: 2 residues within 4Å: Chain D: D.48, S.250 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.48, D:D.48, H2O.52, H2O.54 CA.16: 1 residues within 4Å: Chain D: E.78 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.78, D:E.78, H2O.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abbas, Y.M. et al., Structure of human IFIT1 with capped RNA reveals adaptable mRNA binding and mechanisms for sensing N1 and N2 ribose 2'-O methylations. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-03-01

Peptides

Interferon-induced protein with tetratricopeptide repeats 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Interferon-induced protein with tetratricopeptide repeats 1

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