1NH0: Protease retropepsin

1.03 A structure of HIV-1 protease: inhibitor binding inside and outside the active site. Determined by X-ray diffraction at 1.03 Å resolution. Released 13 Apr 2004.

Method: X-ray diffraction
Resolution: 1.03 Å
Organism: Human immunodeficiency virus 1
Chains: 4
Atoms: 1,937
Mol. weight: 23.42 kDa
Released: 13 Apr 2004

Explore 1NH0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1NH0 contains 4 α-helices and 20 β-strands across 3 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	28	1	2
β-strand	32-33	2	2
β-strand	43-49	7	2
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: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	1
β-strand	10-15	6	3
β-strand	18-24	7	3
β-strand	32-33	2	3
β-strand	42-49	8	3
β-strand	52-66	15	3
β-strand	69-77	9	3
β-strand	84-85	2	3
α-helix	87-90	4
α-helix	91-93	3
β-strand	96-98	3	1

Chain I: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3	1	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protease retropepsin	A, B	protein	99	Human immunodeficiency virus 1	P03367
peptidomimetic inhibitor KI2-PHE-GLU-GLU-NH2	I, J	protein	5

Sequence of entity 1 (A, B), FASTA

>1NH0_1 PROTEASE RETROPEPSIN (chains A, B)
PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYD
QILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Sequence of entity 2 (I, J), FASTA

>1NH0_2 peptidomimetic inhibitor KI2-PHE-GLU-GLU-NH2 (chains I, J)
XFEEX

Primary citation

A Phenylnorstatine Inhibitor Binding to HIV-1 Protease: Geometry, Protonation, and Subsite-Pocket Interactions Analyzed at Atomic Resolution. Brynda, J., Rezacova, P., Fabry, M. et al. J Med Chem (2004) 47:2030-2036. DOI 10.1021/jm031105q · 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
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
2QD7 1.11 Å, HIV-1 Protease Mutant V82A with potent Antiviral inhibitor GRL-98065
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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