MolNFT v1 · #135923 · protein + RNA
IFIT1 monomeric mutant (L457E/L464E) with M7GPPP-aaaa (syn and anti conformations of cap)
5UDI · Interferon-induced protein with tetratricopeptide repeats 1: “IFIT1 monomeric mutant (L457E/L464E) with M7GPPP-aaaa (syn and anti conformations of cap)”. X-ray diffraction, 2 ligands (GTA, CA), 3 pockets (best druggability 0.85).…
- PDB
- 5UDI
- Type
- protein + RNA
- Length
- 463 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interferon-induced protein with tetratricopeptide repeats 1; RNA…
- UniProt
- P09914
- Ligands
- GTA, CA
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interferon-induced protein with tetratricopeptide repeats 1 | protein | 460 | 75% helix, 0% strand | P09914 |
| B | RNA (5'-D(*(GTA))-R(P*AP*AP*A)-3') | rna | 3 | — | — |
Ligands and binding sites
- GTA · P1-7-methylguanosine-P3-adenosine-5',5'-triphosphate · ligand · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 689 | 0.85 | 0.89 | 86 | GTA |
| 2 | 121 | 0.44 | 0.77 | 23 | empty |
| 3 | 62 | 0.30 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 647 Ų buried · 14 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5UDI · IFIT1 monomeric mutant (L457E/L464E) with m7Gppp-AAAA (syn and anti conformations of cap) · the same entry in another collection · chain A against A, TM-score 1.00
- P09914 · AlphaFold monomer V2.0 prediction for interferon-induced protein with tetratricopeptide… · a predicted model of the same protein · chain A against A, TM-score 1.00
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
- Elsewhere: RCSB PDB 5UDI · PDBe 5UDI · UniProt P09914
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