2QD7: Protease

HIV-1 Protease Mutant V82A with potent Antiviral inhibitor GRL-98065. Determined by X-ray diffraction at 1.11 Å resolution. Released 22 Apr 2008.

Method: X-ray diffraction
Resolution: 1.11 Å
Organism: Human immunodeficiency virus 1
Chains: 2
Atoms: 1,917
Mol. weight: 22.53 kDa
Ligands: 065, PO4
Released: 22 Apr 2008

Explore 2QD7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2QD7 contains 3 α-helices and 18 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, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	1
β-strand	10-15	6	2
β-strand	18-24	7	2
β-strand	32-34	3	2
β-strand	43-49	7	2
β-strand	52-66	15	2
β-strand	69-78	10	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, 9 β-strands

Element	Residues	Length	Sheet
β-strand	102-103	2	1
β-strand	110-115	6	3
β-strand	118-124	7	3
β-strand	132-133	2	3
β-strand	142-149	8	3
β-strand	152-166	15	3
β-strand	169-177	9	3
β-strand	184-185	2	3
α-helix	187-190	4
β-strand	196-198	3	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protease	A, B	protein	99	Human immunodeficiency virus 1	P03367

Sequence of entity 1 (A, B), FASTA

>2QD7_1 Protease (chains A, B)
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGIGGFIKVRQYD
QIIIEIAGHKAIGTVLVGPTPANIIGRNLLTQIGATLNF

Ligands and cofactors

ID	Name	Formula	Copies
065	(3R,3AS,6AR)-HEXAHYDROFURO[2,3-b]furan-3-YL(2S,3R)-3-hydroxy-4-(N-isobutylbenzo…	C28 H36 N2 O9 S	1
PO4	Phosphate ion	O4 P	2

Water and common crystallization additives (GOL, DMS) are not listed.

Primary citation

Potent new antiviral compound shows similar inhibition and structural interactions with drug resistant mutants and wild type HIV-1 protease. Wang, Y.F., Tie, Y., Boross, P.I. et al. J Med Chem (2007) 50:4509-4515. DOI 10.1021/jm070482q · PubMed

Other PDB entries of the same protein (UniProt P03367), best resolution first:

5YOK 0.85 Å, Structure of HIV-1 Protease in Complex with Inhibitor KNI-1657
3A2O 0.88 Å, Crystal Structure of HIV-1 Protease Complexed with KNI-1689
3FX5 0.93 Å, Structure of HIV-1 Protease in Complex with Potent Inhibitor KNI-272 Determined by High…
3DJK 1.0 Å, Wild Type HIV-1 Protease with potent Antiviral inhibitor GRL-0255A
1NH0 1.03 Å, 1.03 A structure of HIV-1 protease: inhibitor binding inside and outside the active site
3NDX 1.03 Å, HIV-1 Protease Saquinavir:Ritonavir 1:50 complex structure
3BVA 1.05 Å, Cystal structure of HIV-1 Active Site Mutant D25N and p2-NC analog inhibitor
4HE9 1.06 Å, Crystal Structure of HIV-1 protease mutants I54M complexed with inhibitor GRL-0519
3DK1 1.07 Å, Wild Type HIV-1 Protease with potent Antiviral inhibitor GRL-0105A
3TOH 1.12 Å, HIV-1 Protease - Epoxydic Inhibitor Complex (pH 9 - Orthorombic Crystal form P212121)
8FUJ 1.12 Å, HIV-1 wild type protease with GRL-03419A, with N-(2,5-dimethylphenyl)-4-(pyridin-3-yl)pyr…
7TO5 1.13 Å, HIV-1 wild type protease with GRL-05816A, with C-4 substituted cyclohexane-fused…

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