MolNFT v1 · #135924 · protein + RNA
IFIT1 monomeric mutant (L457E/L464E) with gppp-aaaa
5UDJ · Interferon-induced protein with tetratricopeptide repeats 1: “IFIT1 monomeric mutant (L457E/L464E) with gppp-aaaa”. X-ray diffraction, 2 ligands (G3A, CA), 4 pockets (best druggability 0.85). MolNFT v1 #135924 on GenesisL1: 3D…
- PDB
- 5UDJ
- 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
- G3A, CA
- Pockets
- 4 · 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(*(G3A))-R(P*AP*AP*A)-3') | rna | 3 | — | — |
Ligands and binding sites
- G3A · Guanosine-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
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 749 | 0.85 | 0.88 | 79 | G3A |
| 2 | 91 | 0.40 | 0.77 | 17 | empty |
| 3 | 51 | 0.28 | 0.75 | 16 | empty |
| 4 | 50 | 0.27 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 649 Ų buried · 13 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5UDJ · IFIT1 monomeric mutant (L457E/L464E) with Gppp-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 5UDJ · PDBe 5UDJ · UniProt P09914
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