2A1E | pdb_00002a1e

High resolution structure of HIV-1 PR with TS-126

PDB DOI: https://doi.org/10.2210/pdb2A1E/pdb

Classification: HYDROLASE
Organism(s): Human immunodeficiency virus 1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2005-06-20 Released: 2006-02-21
Deposition Author(s): Demitri, N., Geremia, S., Randaccio, L., Wuerges, J., Benedetti, F., Berti, F., Dinon, F., Campaner, P., Tell, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.201 (Depositor), 0.190 (DCC)
R-Value Work:
0.156 (Depositor), 0.160 (DCC)
R-Value Observed:
0.156 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

A potent HIV protease inhibitor identified in an epimeric mixture by high-resolution protein crystallography.

Geremia, S., Demitri, N., Wuerges, J., Benedetti, F., Berti, F., Tell, G., Randaccio, L.

(2006) ChemMedChem 1: 186-188

PubMed: 16892350 Search on PubMed
DOI: https://doi.org/10.1002/cmdc.200500063
Primary Citation of Related Structures:
2A1E

Organizational Affiliation

Department of Chemical Sciences and Centre of Excellence in Biocrystallography, University of Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy. geremia@univ.trieste.it

Macromolecule Content

Total Structure Weight: 23.05 kDa
Atom Count: 1,917
Modelled Residue Count: 198
Deposited Residue Count: 198
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pol polyprotein	A, B	99	Human immunodeficiency virus 1	Mutation(s): 5 Gene Names: GAG-POL EC: 3.4.23.16
UniProt
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)) Explore P03367 Go to UniProtKB: P03367
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03367
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IPF Query on IPF Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	N-ACETYLTRYPTOPHYL-N~1~-{3-[1-(N-ACETYLTRYPTOPHYLVALYL)PYRROLIDIN-2-YL]-1-BENZYL-2,3-DIHYDROXYPROPYL}VALINAMIDE C₅₀ H₆₄ N₈ O₈ BDIYLIYACVEIHS-QVWIHFFISA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain L [auth B] SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain L [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain D [auth A] mmCIF format, chain L [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	C [auth A], D [auth A], E [auth A], F [auth A], L [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	I [auth B], J [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain I [auth B] Focus chain J [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.201 (Depositor), 0.190 (DCC)
R-Value Work: 0.156 (Depositor), 0.160 (DCC)
R-Value Observed: 0.156 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.269	α = 90
b = 84.956	β = 90
c = 46.061	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
SHELXL-97	refinement
CCP4	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-02-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-02-21
Type: Initial release
Version 1.1: 2007-10-21
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2021-11-10
Changes: Database references, Derived calculations
Version 1.4: 2023-10-25
Changes: Data collection, Refinement description

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Deposit Data

Help and Resources

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High resolution structure of HIV-1 PR with TS-126

A potent HIV protease inhibitor identified in an epimeric mixture by high-resolution protein crystallography.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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