3OY4 | pdb_00003oy4

Crystal Structure of HIV-1 L76V Protease in Complex with the Protease Inhibitor Darunavir.

PDB DOI: https://doi.org/10.2210/pdb3OY4/pdb

Classification: Hydrolase/Hydrolase Inhibitor
Organism(s): HIV-1 M:B_ARV2/SF2
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-09-22 Released: 2011-02-09
Deposition Author(s): Schiffer, C.A., Nalivaika, E.A., Bandaranayake, R.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free:
0.219 (Depositor), 0.230 (DCC)
R-Value Work:
0.178 (Depositor), 0.190 (DCC)
R-Value Observed:
0.180 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of HIV-1 L76V Protease in Complex with the Protease Inhibitor Darunavir.

Schiffer, C.A., Nalivaika, E.A., Bandaranayake, R.M.

To be published.

Macromolecule Content

Total Structure Weight: 22.94 kDa
Atom Count: 1,709
Modeled 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
HIV-1 PROTEASE	A, B	99	HIV-1 M:B_ARV2/SF2	Mutation(s): 2 Gene Names: gag-pol EC: 3.4.23.16
UniProt
Find proteins for P03369 (Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2)) Explore P03369 Go to UniProtKB: P03369
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03369
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
017 Query on 017 Download Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B] mmCIF format, chain N [auth B]	N [auth B]	(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE C₂₇ H₃₇ N₃ O₇ S CJBJHOAVZSMMDJ-HEXNFIEUSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth A], H [auth B], I [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] J [auth B] K [auth B] E [auth A], F [auth A], G [auth A], J [auth B], K [auth B], L [auth B], M [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.219 (Depositor), 0.230 (DCC)
R-Value Work: 0.178 (Depositor), 0.190 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.719	α = 90
b = 57.714	β = 90
c = 62.03	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-02-09

Deposition Author(s):

Schiffer, C.A.

Nalivaika, E.A.

Bandaranayake, R.M.

Revision History (Full details and data files)

Version 1.0: 2011-02-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2024-02-21
Changes: Data collection, Database references, Derived calculations, Structure summary

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Help and Resources

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Crystal Structure of HIV-1 L76V Protease in Complex with the Protease Inhibitor Darunavir.

Crystal Structure of HIV-1 L76V Protease in Complex with the Protease Inhibitor Darunavir.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)

3OY4 | pdb_00003oy4