4U7V: Wild-type HIV protease

Structure of wild-type HIV protease in complex with degraded photosensitive inhibitor. Determined by X-ray diffraction at 1.38 Å resolution. Released 25 Mar 2015.

Method: X-ray diffraction
Resolution: 1.38 Å
Organism: Human immunodeficiency virus 1
Chains: 2
Atoms: 1,830
Mol. weight: 22.29 kDa
Ligands: 3EN
Released: 25 Mar 2015

Explore 4U7V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4U7V contains 3 α-helices and 20 β-strands across 2 chains. 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: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	1
β-strand	10-15	6	2
β-strand	18-24	7	2
β-strand	32-33	2	2
β-strand	43-49	7	2
β-strand	51	1	3
β-strand	52-66	15	2
β-strand	69-77	9	2
β-strand	84-85	2	2
α-helix	87-90	4
α-helix	91-93	3
β-strand	96-98	3	1

Chain B: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	1
β-strand	10-15	6	4
β-strand	18-24	7	4
β-strand	32-33	2	4
β-strand	43-49	7	4
β-strand	51	1	3
β-strand	52-66	15	4
β-strand	69-77	9	4
β-strand	84-85	2	4
α-helix	87-90	4
β-strand	96-98	3	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
V-1 protease	A, B	protein	99	Human immunodeficiency virus 1	P04585 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4U7V_1 V-1 protease (chains A, B)
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGIGGFIKVRQYD
QIIIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Ligands and cofactors

ID	Name	Formula	Copies
3EN	N-[(2S,4S,5S)-4-hydroxy-1,6-diphenyl-5-{[(1,3-thiazol-5-ylmethoxy)carbonyl]amin…	C28 H36 N4 O4 S	1

Water and common crystallization additives (BME) are not listed.

Primary citation

Triggering HIV polyprotein processing by light using rapid photodegradation of a tight-binding protease inhibitor. Schimer, J., Pavova, M., Anders, M. et al. Nat Commun (2015) 6:6461-6461. DOI 10.1038/ncomms7461 · PubMed

Other PDB entries of the same protein (UniProt P04585 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6DV4 1.14 Å, HIV-1 wild type protease with GRL-04315A, a tetrahydronaphthalene carboxamide with…
6DIF 1.2 Å, Wild-type HIV-1 protease in complex with tipranavir
6DV0 1.2 Å, HIV-1 wild type protease with GRL-02815A, a thiochroman heterocycle with (S)-Boc-amine…
5DGU 1.22 Å, Crystal Structure of HIV-1 Protease Inhibitors Containing Substituted…
6E9A 1.22 Å, HIV-1 wild type protease with grl-034-17A, (3aS, 5R, 6aR)-2-oxohexahyd…
6DJ1 1.26 Å, Wild-type HIV-1 protease in complex with Lopinavir
8F0F 1.29 Å, HIV-1 wild type protease with GRL-110-19A, a chloroacetamide derivative based on…
6E7J 1.3 Å, HIV-1 wild type protease with GRL-042-17A, 3-phenylhexahydro-2h-cyclopenta[d]oxazol-2-one…
6DJ7 1.31 Å, HIV-1 protease with mutation L76V in complex with GRL-5010…
8ESX 1.35 Å, HIV protease in complex with benzoxaborolone analog of darunavir
8ESY 1.35 Å, D30N mutant HIV protease in complex with benzoxaborolone analog of darunavir
6DJ2 1.36 Å, HIV-1 protease with single mutation L76V in complex with Lopinavir

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