3SA8 | pdb_00003sa8

Crystal structure of wild-type HIV-1 protease in complex with KB83

PDB DOI: https://doi.org/10.2210/pdb3SA8/pdb

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

Deposited: 2011-06-02 Released: 2012-06-06
Deposition Author(s): Schiffer, C.A., Nalam, M.N.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.193 (Depositor), 0.199 (DCC)
R-Value Work:
0.164 (Depositor), 0.174 (DCC)
R-Value Observed:
0.165 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Protease Inhibitors that protrude out from substrate envelope are more susceptible to developing drug resistance

Altman, M.D., Nalam, M.N.L., Ali, A., Cao, H., Rana, T.M., Schiffer, C.A., Tidor, B.

To be published.

Macromolecule Content

Total Structure Weight: 22.66 kDa
Atom Count: 1,841
Modeled Residue Count: 198
Deposited Residue Count: 198
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A, B	99	Human immunodeficiency virus 1	Mutation(s): 1 Gene Names: gag-pol, pol
UniProt
Find proteins for O38732 (Human immunodeficiency virus type 1) Explore O38732 Go to UniProtKB: O38732
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O38732
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K83 Query on K83 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	3-hydroxy-N-[(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}-1-phenylbutan-2-yl]benzamide C₂₈ H₃₄ N₂ O₆ S QMZQZXVEFMMDKK-RRPNLBNLSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A], H [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain F [auth A] Focus chain I [auth B]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000951 (K83) Query on PRD_000951	G [auth A]	3-HYDROXY-N-[(2S,3R)-3-HYDROXY-4-{[(4-METHOXYPHENYL)SULFONYL](2-METHYLPROPYL)AMINO}-1-PHENYLBUTAN-2-YL]BENZAMIDE	Peptide-like / Inhibitor		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.193 (Depositor), 0.199 (DCC)
R-Value Work: 0.164 (Depositor), 0.174 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.731	α = 90
b = 57.739	β = 90
c = 61.769	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
BioCARS-developed	data collection
HKL-2000	data reduction
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-06-06

Deposition Author(s):

Schiffer, C.A.

Nalam, M.N.L.

Revision History (Full details and data files)

Version 1.0: 2012-06-06
Type: Initial release
Version 1.1: 2012-12-12
Changes: Other
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description