6MCR: Wild type HIV-1 protease

X-ray crystal structure of wild type HIV-1 protease in complex with GRL-001. Determined by X-ray diffraction at 1.48 Å resolution. Released 24 Apr 2019.

Method: X-ray diffraction
Resolution: 1.48 Å
Organism: Human immunodeficiency virus 1
Chains: 1
Atoms: 870
Mol. weight: 11.71 kDa
Ligands: JDY
Released: 24 Apr 2019

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

Secondary structure: helices and β-sheets

6MCR contains 2 α-helices 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: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	10-15	6	1
β-strand	18-24	7	1
β-strand	32-33	2	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
α-helix	91-93	3

Molecules and chains

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

Sequence of entity 1 (A), FASTA

>6MCR_1 Protease (chains A)
PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYD
QILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Ligands and cofactors

ID	Name	Formula	Copies
JDY	(3S,3aR,5R,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl…	C33 H41 F N4 O7 S2	1

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

Primary citation

Halogen Bond Interactions of Novel HIV-1 Protease Inhibitors (PI) (GRL-001-15 and GRL-003-15) with the Flap of Protease Are Critical for Their Potent Activity against Wild-Type HIV-1 and Multi-PI-Resistant Variants. Hattori, S.I., Hayashi, H., Bulut, H. et al. Antimicrob Agents Chemother (2019) 63. DOI 10.1128/AAC.02635-18 · 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
6OYD 1.46 Å, X-ray crystal structure of wild type HIV-1 protease in complex with GRL-004
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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