Research workbench
Structural basis for preferential recognition of cap 0 RNA by a human IFIT1-IFIT3 protein complex
Analyse Structural basis for preferential recognition of cap 0 RNA by a human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C6K
- Type
- protein + RNA
- Length
- 1,018 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interferon-induced protein with tetratricopeptide repeats 1; Interferon-induced protein…
- UniProt
- P09914, O14879
- Ligands
- M7G, MG
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interferon-induced protein with tetratricopeptide repeats 1 | protein | 456 | 75% helix, 0% strand | P09914 |
| B | Interferon-induced protein with tetratricopeptide repeats 1 | protein | 454 | 75% helix, 0% strand | P09914 |
| C, D | Interferon-induced protein with tetratricopeptide repeats 3 | protein | 44 | 73% helix, 0% strand | O14879 |
| E, F | RNA (5'-R((M7G)*P*AP*UP*AP*GP*GP*CP*GP*GP*CP*G)-3') | rna | 10 | — | — |
Ligands and binding sites
- M7G · 7N-methyl-8-hydroguanosine-5'-diphosphate · ligand · 2 copies · chains A, E, B, F
- MG · Magnesium ion · metal · 4 copies · chains B, F, A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 656 | 0.81 | 0.85 | 72 | M7G |
| 2 | 235 | 0.78 | 0.92 | 33 | empty |
| 3 | 360 | 0.77 | 0.87 | 53 | M7G |
| 4 | 256 | 0.76 | 0.90 | 36 | MG |
| 5 | 144 | 0.61 | 0.85 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–E · 1304 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–F · 1256 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–B · 720 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 339 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 318 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6C6K · Structural basis for preferential recognition of cap 0 RNA by a human IFIT1-IFIT3 protein… · the same entry in another collection · chain E against E, TM-score 1.00
- P09914 · AlphaFold monomer V2.0 prediction for interferon-induced protein with tetratricopeptide… · a predicted model of the same protein · chain B against A, TM-score 0.99
- O14879 · AlphaFold monomer V2.0 prediction for interferon-induced protein with tetratricopeptide… · a predicted model of the same protein · chain C against A, TM-score 0.66
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P09914
- Every structure of UniProt O14879
- Elsewhere: RCSB PDB 6C6K · PDBe 6C6K · UniProt P09914 · UniProt O14879
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