Research workbench

Human IFIT1 dimer with M7GPPP-aaaa

Analyse Human IFIT1 dimer with M7GPPP-aaaa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5W5H
Type: protein + RNA
Length: 903 residues
Chains: 4
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
Pockets: 9 · best druggability 0.85

Structure

x-ray diffraction · 3 distinct chains · 75% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Interferon-induced protein with tetratricopeptide repeats 1	protein	451	74% helix, 0% strand	P09914
B, D	RNA (5'-D((GTA))-R(PAPAPA)-3')	rna	3	—	—
C	Interferon-induced protein with tetratricopeptide repeats 1	protein	446	75% helix, 0% strand	P09914

Ligands and binding sites

GTA · P1-7-methylguanosine-P3-adenosine-5',5'-triphosphate · ligand · 2 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	742	0.85	0.88	90	GTA
2	819	0.84	0.86	99	GTA
3	122	0.43	0.76	16	empty
4	111	0.39	0.75	13	empty
5	75	0.35	0.76	26	empty

Interfaces

3 interfaces between chains.

C–D · 654 Å² buried · 15 hydrogen bonds · protein-nucleic
A–B · 642 Å² buried · 15 hydrogen bonds · protein-nucleic
A–C · 537 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

5W5H · Human IFIT1 dimer with m7Gppp-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 C 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 5W5H · PDBe 5W5H · UniProt P09914

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.