3EM4 | pdb_00003em4

Crystal structure of atazanavir (ATV) in complex with I50L/A71V drug-resistant HIV-1 protease

PDB DOI: https://doi.org/10.2210/pdb3EM4/pdb

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

Deposited: 2008-09-23 Released: 2009-09-01
Deposition Author(s): Prabu-Jeyabalan, M., King, N., Royer, C., Schiffer, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.249 (Depositor), 0.250 (DCC)
R-Value Work:
0.179 (Depositor), 0.188 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

Kinetic and Structural studies on atazanavir-specific I50L drug-resistant HIV-1 protease mutant

Prabu-Jeyabalan, M., King, N., Bandaranayake, R., Nalivaika, E., Schiffer, C.

To be published.

Macromolecule Content

Total Structure Weight: 45.39 kDa
Atom Count: 3,230
Modeled Residue Count: 396
Deposited Residue Count: 396
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A, B, C [auth U], D [auth V]	99	HIV-1 M:B_ARV2/SF2	Mutation(s): 3 Gene Names: gag-pol, HIV-1 subtype B 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03369
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DR7 Query on DR7 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth V] MOL2 format, chain E [auth A] MOL2 format, chain K [auth V] mmCIF format, chain E [auth A] mmCIF format, chain K [auth V]	E [auth A], K [auth V]	(3S,8S,9S,12S)-3,12-BIS(1,1-DIMETHYLETHYL)-8-HYDROXY-4,11-DIOXO-9-(PHENYLMETHYL)-6-[[4-(2-PYRIDINYL)PHENYL]METHYL]-2,5, 6,10,13-PENTAAZATETRADECANEDIOIC ACID DIMETHYL ESTER C₃₈ H₅₂ N₆ O₇ AXRYRYVKAWYZBR-GASGPIRDSA-N		Interactions Focus chain E [auth A] Focus chain K [auth V] Interactions & Density Focus chain E [auth A] Focus chain K [auth V]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth U] SDF format, chain L [auth V] SDF format, chain M [auth V] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth U] MOL2 format, chain L [auth V] MOL2 format, chain M [auth V] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth U] mmCIF format, chain L [auth V] mmCIF format, chain M [auth V]	F [auth A] G [auth B] H [auth B] I [auth B] J [auth U] F [auth A], G [auth B], H [auth B], I [auth B], J [auth U], L [auth V], M [auth V]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth U] Focus chain L [auth V] Focus chain M [auth V] Interactions & Density Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth U] Focus chain L [auth V] Focus chain M [auth V]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.249 (Depositor), 0.250 (DCC)
R-Value Work: 0.179 (Depositor), 0.188 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.231	α = 90
b = 59.54	β = 82.22
c = 59.863	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-09-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-09-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2017-10-25
Changes: Advisory, Refinement description
Version 1.3: 2018-01-24
Changes: Database references
Version 1.4: 2021-10-20
Changes: Advisory, Database references, Derived calculations, Structure summary
Version 1.5: 2023-09-06
Changes: Data collection, Refinement description
Version 1.6: 2024-03-13
Changes: Source and taxonomy, Structure summary