6OYD: Wild type HIV-1 protease

X-ray crystal structure of wild type HIV-1 protease in complex with GRL-004. Determined by X-ray diffraction at 1.46 Å resolution. Released 20 May 2020.

Method: X-ray diffraction
Resolution: 1.46 Å
Organism: Human immunodeficiency virus 1
Chains: 1
Atoms: 849
Mol. weight: 11.51 kDa
Ligands: NKA
Released: 20 May 2020

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

Secondary structure: helices and β-sheets

6OYD contains 1 α-helix and 7 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: 1 helix, 7 β-strands

Element	Residues	Length	Sheet
β-strand	10-15	6	1
β-strand	18-24	7	1
β-strand	31-33	3	1
β-strand	43-49	7	1
β-strand	52-66	15	1
β-strand	69-77	9	1
β-strand	84-85	2	1
α-helix	87-90	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protease	A	protein	99	Human immunodeficiency virus 1	P12497

Sequence of entity 1 (A), FASTA

>6OYD_1 Protease (chains A)
PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYD
QILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Ligands and cofactors

ID	Name	Formula	Copies
NKA	(3S,3aR,5R,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl…	C33 H43 F N4 O8 S	1

Primary citation

Single atom changes in newly synthesized HIV protease inhibitors reveal structural basis for extreme affinity, high genetic barrier, and adaptation to the HIV protease plasticity. Bulut, H., Hattori, S.I., Aoki-Ogata, H. et al. Sci Rep (2020) 10:10664-10664. DOI 10.1038/s41598-020-65993-z · 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)
6T6E 1.3 Å, Crystal Structure of the C-terminal domain of the HIV-1 Integrase (PNL4-3)
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
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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