8VC0 | pdb_00008vc0

HIV-1 CA crosslinked pentamer in complex with GS-CA1

PDB DOI: https://doi.org/10.2210/pdb8VC0/pdb

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

Deposited: 2023-12-13 Released: 2025-03-19
Deposition Author(s): Piacentini, J., Ganser-Pornillos, B.K., Pornillos, O.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.46 Å
R-Value Free:
0.315 (Depositor), 0.314 (DCC)
R-Value Work:
0.257 (Depositor), 0.257 (DCC)
R-Value Observed:
0.260 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structure of disulfide-stabilized HIV-1 CA pentamer in complex with the ultra-potent capsid inhibitor, GS-CA1

Piacentini, J., Ganser-Pornillos, B.K., Pornillos, O.

To be published.

Macromolecule Content

Total Structure Weight: 264.35 kDa
Atom Count: 14,963
Modeled Residue Count: 1,997
Deposited Residue Count: 2,310
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein p24	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	231	Human immunodeficiency virus 1	Mutation(s): 4 Gene Names: gag-pol
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12497 Go to UniProtKB: P12497
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P12497
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1AAO (Subject of Investigation/LOI) Query on A1AAO Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain M [auth C] SDF format, chain O [auth E] SDF format, chain P [auth F] SDF format, chain Q [auth G] SDF format, chain R [auth H] SDF format, chain S [auth I] SDF format, chain T [auth J] SDF format, chain N [auth D] SDF format, chain L [auth B] MOL2 format, chain K [auth A] MOL2 format, chain M [auth C] MOL2 format, chain O [auth E] MOL2 format, chain P [auth F] MOL2 format, chain Q [auth G] MOL2 format, chain R [auth H] MOL2 format, chain S [auth I] MOL2 format, chain T [auth J] MOL2 format, chain N [auth D] MOL2 format, chain L [auth B] mmCIF format, chain K [auth A] mmCIF format, chain M [auth C] mmCIF format, chain O [auth E] mmCIF format, chain P [auth F] mmCIF format, chain Q [auth G] mmCIF format, chain R [auth H] mmCIF format, chain S [auth I] mmCIF format, chain T [auth J] mmCIF format, chain N [auth D] mmCIF format, chain L [auth B]	K [auth A] L [auth B] M [auth C] N [auth D] O [auth E] K [auth A], L [auth B], M [auth C], N [auth D], O [auth E], P [auth F], Q [auth G], R [auth H], S [auth I], T [auth J]	N-[(1S)-1-{(3M)-3-{4-chloro-3-[(cyclopropanesulfonyl)amino]-1-(2,2-difluoroethyl)-1H-indazol-7-yl}-6-[3-(methanesulfonyl)-3-methylbut-1-yn-1-yl]pyridin-2-yl}-2-(3,5-difluorophenyl)ethyl]-2-[(3bS,4aR)-3-(difluoromethyl)-5,5-difluoro-3b,4,4a,5-tetrahydro-1H-cyclopropa[3,4]cyclopenta[1,2-c]pyrazol-1-yl]acetamide C₄₁ H₃₆ Cl F₈ N₇ O₅ S₂ CPCUUUACFKQOHY-GKRYNVPLSA-N		Interactions Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth F] Focus chain Q [auth G] Focus chain R [auth H] Focus chain S [auth I] Focus chain T [auth J] Interactions & Density Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth F] Focus chain Q [auth G] Focus chain R [auth H] Focus chain S [auth I] Focus chain T [auth J]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.46 Å
R-Value Free: 0.315 (Depositor), 0.314 (DCC)
R-Value Work: 0.257 (Depositor), 0.257 (DCC)
R-Value Observed: 0.260 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.403	α = 90
b = 149.456	β = 90
c = 157.109	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-03-19

Deposition Author(s):

Piacentini, J.

Ganser-Pornillos, B.K.

Pornillos, O.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R21AI167756
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U54AI170856