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HIV-1 integrase catalytic core and C-terminal domain

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

PDB: 1EX4
Type: protein
Length: 416 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Integrase
UniProt: P04585
Ligands: CPS
Pockets: 5 · best druggability 0.60

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Integrase	protein	212	41% helix, 25% strand	P04585
B	Integrase	protein	204	41% helix, 29% strand	P04585

Ligands and binding sites

CPS · 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate · ligand · 4 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	126	0.60	0.85	26	empty
2	265	0.58	0.78	33	empty
3	145	0.44	0.76	28	empty
4	127	0.42	0.75	17	empty
5	85	0.32	0.74	14	empty

Interfaces

1 interface between chains.

A–B · 1730 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

1EX4 · HIV-1 integrase catalytic core and C-terminal 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 P04585
Elsewhere: RCSB PDB 1EX4 · PDBe 1EX4 · UniProt P04585

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