6T6E: C-terminal domain of the HIV-1 Integrase

Crystal Structure of the C-terminal domain of the HIV-1 Integrase (PNL4-3). Determined by X-ray diffraction at 1.3 Å resolution. Released 22 Jul 2020.

Method: X-ray diffraction
Resolution: 1.3 Å
Organism: Human immunodeficiency virus 1
Chains: 1
Atoms: 543
Mol. weight: 7.08 kDa
Ligands: NI
Released: 22 Jul 2020

Explore 6T6E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6T6E contains 3 α-helices and 6 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	218-220	3
β-strand	223-227	5	1
α-helix	235	1
β-strand	236-239	4	1
β-strand	240-244	5	2
β-strand	248-253	6	2
β-strand	256-261	6	2
α-helix	262-264	3
β-strand	265-269	5	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Pol protein	A	protein	59	Human immunodeficiency virus 1	P12497

Sequence of entity 1 (A), FASTA

>6T6E_1 Pol protein (chains A)
MGHHHHHHIQNFRVYYRDSRDPVWKGPAKLLWKGEGAVVIQDNSDIKVVPRRKAKIIRD

Ligands and cofactors

ID	Name	Formula	Copies
NI	Nickel (II) ion	Ni	1

Primary citation

NKNK: a New Essential Motif in the C-Terminal Domain of HIV-1 Group M Integrases. Kanja, M., Cappy, P., Levy, N. et al. J Virol (2020) 94. DOI 10.1128/JVI.01035-20 · PubMed

Other PDB entries of the same protein (UniProt P12497), best resolution first:

3DS4 1.12 Å, HIV-1 capsid C-terminal domain mutant (L211S) in complex with an inhibitor of particle…
3DS2 1.2 Å, HIV-1 capsid C-terminal domain mutant (Y169A)
2XDE 1.4 Å, Crystal structure of the complex of PF-3450074 with an engineered HIV capsid N terminal…
3L3U 1.4 Å, Crystal structure of the HIV-1 integrase core domain to 1.4A
2PWO 1.45 Å, Crystal Structure of HIV-1 CA146 A92E Psuedo Cell
3WNF 1.45 Å, Cyclic hexapeptide CKIDNC in complex with HIV-1 integrase
6OYD 1.46 Å, X-ray crystal structure of wild type HIV-1 protease in complex with GRL-004
6MCR 1.48 Å, X-ray crystal structure of wild type HIV-1 protease in complex with GRL-001
2PXR 1.5 Å, Crystal Structure of HIV-1 CA146 in the Presence of CAP-1
3WNH 1.5 Å, Cyclic hexapeptide PKZDNv in complex with HIV-1 integrase
4NX4 1.5 Å, Re-refinement of CAP-1 HIV-CA complex
6MCS 1.52 Å, X-ray crystal structure of wild type HIV-1 protease in complex with GRL-003

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