Research workbench
IFIT1 monomeric mutant (L457E/L464E) with ppp-aaaa
Analyse IFIT1 monomeric mutant (L457E/L464E) with ppp-aaaa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UDK
- Type
- protein + RNA
- Length
- 465 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
- CA
- Pockets
- 5 · best druggability 0.74
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 | 461 | 75% helix, 0% strand | P09914 |
| B | RNA (5'-D(*(ATP))-R(P*AP*AP*A)-3') | rna | 4 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 302 | 0.74 | 0.87 | 38 | PGE, PEG, EDO |
| 2 | 106 | 0.74 | 0.95 | 28 | empty |
| 3 | 99 | 0.40 | 0.76 | 16 | empty |
| 4 | 85 | 0.34 | 0.74 | 20 | empty |
| 5 | 70 | 0.32 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 990 Ų buried · 25 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 5UDK · IFIT1 monomeric mutant (L457E/L464E) with PPP-AAAA · 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 0.99
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 5UDK · PDBe 5UDK · UniProt P09914
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