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Structure of a protein-modified aptamer complex

Analyse Structure of a protein-modified aptamer complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7MK1
Type: protein + DNA
Length: 324 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antiviral innate immune response receptor rig-I; DNA (41-mer)
EC: 3.6.4.13
UniProt: O95786
Ligands: ZN, MG
Pockets: 6 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 13% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Antiviral innate immune response receptor rig-I (EC 3.6.4.13)	protein	121	13% helix, 46% strand	O95786
C, D	DNA (41-mer)	dna	41	—	—

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, C, B, D

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

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	620	0.71	0.79	59	empty
2	202	0.59	0.81	20	empty
3	196	0.50	0.77	27	empty
4	83	0.40	0.79	18	empty
5	95	0.36	0.75	8	empty

Interfaces

5 interfaces between chains.

A–C · 870 Å² buried · 15 hydrogen bonds · protein-nucleic
B–D · 827 Å² buried · 19 hydrogen bonds · protein-nucleic
A–B · 408 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 160 Å² buried · 1 hydrogen bond · protein-nucleic
B–C · 102 Å² buried · 0 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 32 modified (nucleotide modification).

Compared structures

7MK1 · Structure of a protein-modified aptamer complex · the same entry in another collection · chain A against A, TM-score 1.00
O95786 · AlphaFold monomer V2.0 prediction for antiviral innate immune response receptor rig-I… · a predicted model of the same protein · chain B against A, TM-score 0.98

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 O95786
Elsewhere: RCSB PDB 7MK1 · PDBe 7MK1 · UniProt O95786

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