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Solution structure of a ultra-high affinity macrocycle bound to HIV-1 tar RNA

Analyse Solution structure of a ultra-high affinity macrocycle bound to HIV-1 tar RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6D2U
Type: protein + RNA
Length: 43 residues
Chains: 2
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dab-val-arg-thr-arg-lys-gly-arg-arg-ile-nor-ile-dpr-pro; RNA (29-mer)
Pockets: 1 · best druggability 0.46

Structure

solution nmr · 2 distinct chains · 0% helix, 57% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dab-val-arg-thr-arg-lys-gly-arg-arg-ile-nor-ile-dpr-pro	protein	14	0% helix, 57% strand	—
B	RNA (29-mer)	rna	29	—	—

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	190	0.46	0.75	20	empty

Interfaces

1 interface between chains.

A–B · 816 Å² buried · 26 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 modified, 1 d-amino (nonstandard, D-amino acid).

Compared structures

6D2U · Solution structure of a ultra-high affinity macrocycle bound to HIV-1 TAR RNA · the same entry in another collection · 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
Elsewhere: RCSB PDB 6D2U · PDBe 6D2U

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