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HIV-1 integrase core domain complexed with mg++

Analyse HIV-1 integrase core domain complexed with mg++ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1BIU
Type: protein
Length: 439 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HIV-1 integrase
UniProt: P12497
Ligands: MG
Pockets: 9 · best druggability 0.49

Structure

x-ray diffraction · 2 distinct chains · 53% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HIV-1 integrase	protein	147	54% helix, 22% strand	P12497
B, C	HIV-1 integrase	protein	146	51% helix, 22% strand	P12497

Ligands and binding sites

MG · Magnesium ion · metal · 3 copies · chains A, B, C

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

Pockets

9 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	141	0.49	0.78	18	empty
2	111	0.45	0.78	16	empty
3	123	0.45	0.77	23	empty
4	106	0.44	0.78	23	empty
5	119	0.43	0.77	16	empty

Interfaces

2 interfaces between chains.

A–B · 1554 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 218 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1BIU · HIV-1 integrase core domain complexed with mg++ · 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 P12497
Elsewhere: RCSB PDB 1BIU · PDBe 1BIU · UniProt P12497

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