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Excited state (bound-like) sampled during rdc restrained replica- averaged metadynamics (ram) simulations of the HIV-1 tar complexed with cyclic peptide mimetic of tat

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PDB: 5J1O
Type: protein + RNA
Length: 43 residues
Chains: 2
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cyclic peptide mimetic of tat; Apical region (29MER) of the HIV-1 tar element
Pockets: 1 · best druggability 0.43

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cyclic peptide mimetic of tat	protein	14	0% helix, 57% strand	—
B	Apical region (29MER) of the HIV-1 tar element	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	165	0.43	0.75	23	empty

Interfaces

1 interface between chains.

A–B · 707 Å² buried · 21 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 d-amino (D-amino acid).

Compared structures

5J1O · Excited state (Bound-like) sampled during RDC restrained Replica-averaged Metadynamics… · 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 5J1O · PDBe 5J1O

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