3D1X: HIV-1 mutant I54M and inhibitor saquinavir

Crystal structure of HIV-1 mutant I54M and inhibitor saquinavir. Determined by X-ray diffraction at 1.05 Å resolution. Released 3 Jun 2008.

Method: X-ray diffraction
Resolution: 1.05 Å
Organism: Human immunodeficiency virus type 1
Chains: 2
Atoms: 2,023
Mol. weight: 22.39 kDa
Ligands: ROC
Released: 3 Jun 2008

Explore 3D1X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3D1X 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	2-3	2	1
β-strand	10-15	6	2
β-strand	18-24	7	2
β-strand	32-33	2	2
β-strand	42-49	8	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: 1 helix, 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	43-49	7	3
β-strand	52-66	15	3
β-strand	69-77	9	3
β-strand	84-85	2	3
α-helix	87-90	4
β-strand	96-98	3	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HIV-1 Protease	A, B	protein	99	Human immunodeficiency virus type 1	P04587

Sequence of entity 1 (A, B), FASTA

>3D1X_1 HIV-1 Protease (chains A, B)
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGIGGFMKVRQYD
QIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF

Ligands and cofactors

ID	Name	Formula	Copies
ROC	(2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-oc…	C38 H50 N6 O5	1

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

Primary citation

Effect of flap mutations on structure of HIV-1 protease and inhibition by saquinavir and darunavir. Liu, F., Kovalevsky, A.Y., Tie, Y. et al. J Mol Biol (2008) 381:102-115. DOI 10.1016/j.jmb.2008.05.062 · PubMed

Other PDB entries of the same protein (UniProt P04587), best resolution first:

2NMZ 0.97 Å, Crystal structure analysis of HIV-1 protease mutant V82A with a inhibitor saquinavir
3D1Y 1.05 Å, Crystal structure of HIV-1 mutant I54V and inhibitor SAQUINA
3D20 1.05 Å, Crystal structure of HIV-1 mutant I54V and inhibitor DARUNAVIA
2AOG 1.1 Å, Crystal structure analysis of HIV-1 protease mutant V82A with a substrate analog P2-NC
2AVM 1.1 Å, Kinetics, stability, and structural changes in high resolution crystal structures of…
2AVO 1.1 Å, Kinetics, stability, and structural changes in high resolution crystal structures of…
2AVS 1.1 Å, kinetics, stability, and structural changes in high resolution crystal structures of…
2NMY 1.1 Å, Crystal structure analysis of HIV-1 protease mutant V82A with a inhibitor saquinavir
3OXC 1.16 Å, Wild Type HIV-1 Protease with Antiviral Drug Saquinavir
1K1T 1.2 Å, Combining Mutations in HIV-1 Protease to Understand Mechanisms of Resistance
2NNP 1.2 Å, Crystal structure analysis of HIV-1 protease mutant I84V with a inhibitor saquinavir
3CYX 1.2 Å, Crystal structure of HIV-1 mutant I50V and inhibitor saquinavira

Browse structure collections

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