1SP5 | pdb_00001sp5

Crystal structure of HIV-1 protease complexed with a product of autoproteolysis

PDB DOI: https://doi.org/10.2210/pdb1SP5/pdb

Classification: HYDROLASE
Organism(s): Human immunodeficiency virus 1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2004-03-16 Released: 2005-07-19
Deposition Author(s): Vondrackova, E., Hasek, J., Jaskolski, M., Rezacova, P., Dohnalek, J., Skalova, T., Petrokova, H., Duskova, J., Brynda, J., Sedlacek, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.211 (Depositor), 0.174 (DCC)
R-Value Work:
0.177 (Depositor), 0.179 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Product of enzymatic self-cleavage bound in the active site of HIV protease

Vondrackova, E., Hasek, J., Jaskolski, M., Rezacova, P., Dohnalek, J., Skalova, T., Petrokova, H., Duskova, J., Brynda, J., Sedlacek, J.

To be published.

Macromolecule Content

Total Structure Weight: 22.68 kDa
Atom Count: 1,721
Modeled Residue Count: 203
Deposited Residue Count: 203
Unique protein chains: 2

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): 0 Gene Names: 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03367
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
5-mer peptide from Protease	C [auth I]	5	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: POL
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
UniProt Group	P03367
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BME Query on BME Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], J [auth B]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.211 (Depositor), 0.174 (DCC)
R-Value Work: 0.177 (Depositor), 0.179 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.765	α = 90
b = 86.284	β = 90
c = 45.834	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2005-07-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-07-19
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description