7LEF

HIV-1 Protease WT (NL4-3) in Complex with PU7 (LR3-67)

PDB DOI: https://doi.org/10.2210/pdb7LEF/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Human immunodeficiency virus 1
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2021-01-14 Released: 2022-01-26
Deposition Author(s): Lockbaum, G.J., Rusere, L.N., Henes, M., Kosovrasti, K., Lee, S.K., Spielvogel, E., Nalivaika, E.A., Swanstrom, R., KurtYilmaz, N., Schiffer, C.A., Ali, A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free: 0.245
R-Value Work: 0.204
R-Value Observed: 0.206

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

HIV-1 Protease Inhibitors with a P1 Phosphonate Modification Maintain Potency against Drug Resistant Variants by Increased van der Waals Contacts with Flaps Residues

Lockbaum, G.J., Rusere, L.N., Henes, M., Kosovrasti, K., Lee, S.K., Spielvogel, E., Nalivaika, E.A., Swanstrom, R., KurtYilmaz, N., Schiffer, C.A., Ali, A.

To be published.

Macromolecule Content

Total Structure Weight: 23.09 kDa
Atom Count: 1,709
Modelled Residue Count: 198
Deposited Residue Count: 198
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A [auth B], B [auth A]	99	Human immunodeficiency virus 1	Mutation(s): 1 Gene Names: pol
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12497 Go to UniProtKB: P12497
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P12497
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XVS (Subject of Investigation/LOI) Query on XVS Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	diethyl [(4-{(2S,3R)-4-{(2-ethylbutyl)[(4-methoxyphenyl)sulfonyl]amino}-2-[({[(3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl]oxy}carbonyl)amino]-3-hydroxybutyl}phenoxy)methyl]phosphonate C₃₅ H₅₃ N₂ O₁₂ P S GKYSQDWEWYGVFQ-GYLADCCPSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth B] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain C [auth B] MOL2 format, chain D [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain C [auth B] mmCIF format, chain D [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	C [auth B] D [auth B] E [auth A] F [auth A] G [auth A] C [auth B], D [auth B], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]