MolNFT v1 · #110588 · protein

Cyclic hexapeptide CYC[NDPOPPKID] in complex with HIV-1 integrase core domain

4Y1C: “Cyclic hexapeptide CYC[NDPOPPKID] in complex with HIV-1 integrase core domain”. X-ray diffraction, 2 ligands (CD, SO4), 3 pockets (best druggability 0.50). MolNFT v1 #110588 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4Y1C
Type: protein
Length: 292 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Integrase; Cyclic hexapeptide CYC[NDPOPPKID]
UniProt: Q76353
Ligands: CD, SO4
Pockets: 3 · best druggability 0.50

Structure

x-ray diffraction · 3 distinct chains · 46% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Integrase	protein	145	46% helix, 24% strand	Q76353
B	Integrase	protein	141	49% helix, 23% strand	Q76353
C	Cyclic hexapeptide CYC[NDPOPPKID]	protein	6	0% helix, 0% strand	—

Ligands and binding sites

CD · Cadmium ion · metal · 4 copies · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	119	0.50	0.80	18	empty
2	96	0.44	0.79	20	empty
3	90	0.43	0.79	17	empty

Interfaces

3 interfaces between chains.

A–B · 1542 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 222 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 188 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

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

Compared structures

4Y1C · Cyclic hexapeptide cyc[NdPopPKID] in complex with HIV-1 integrase core domain · 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 4Y1C · PDBe 4Y1C · UniProt Q76353

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