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HIV-1 integrase catalytic core domain (ccd) in complex with a fragment-derived allosteric inhibitor

Analyse HIV-1 integrase catalytic core domain (ccd) in complex with a fragment-derived… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5KRT
Type: protein
Length: 145 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Integrase
UniProt: Q76353
Ligands: 6W6
Pockets: 1 · best druggability 0.28

Structure

x-ray diffraction · 1 distinct chain · 50% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Integrase	protein	145	50% helix, 19% strand	Q76353

Ligands and binding sites

6W6 · 3-[2,5-bis(chloranyl)pyrrol-1-yl]thiophene-2-carboxylic acid · ligand · 2 copies · chains A

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

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	55	0.28	0.75	12	empty

Modifications

Observed in the structure: 2 modified (nonstandard).

Compared structures

5KRT · HIV-1 Integrase Catalytic Core Domain (CCD) in Complex with a Fragment-Derived Allosteric… · 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
Every structure of UniProt Q76353
Elsewhere: RCSB PDB 5KRT · PDBe 5KRT · UniProt Q76353

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