5CYM

HIV-1 reverse transcriptase complexed with 4-iodopyrazole

• PDB DOI: https://doi.org/10.2210/pdb5CYM/pdb

• Classification: TRANSFERASE
• Organism(s): Human immunodeficiency virus type 1 BH10
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-07-30 Released: 2015-12-30 
• Deposition Author(s): Bauman, J.D., Arnold, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.229 
• R-Value Work: 0.195 
• R-Value Observed: 0.196 

Literature

Rapid experimental SAD phasing and hot spot identification with halogenated fragments

Bauman, J.D., Harrison, J.J.E.K., Arnold, E.

(2016) IUCrJ 3: 51-60

• DOI: https://doi.org/10.1107/S2052252515021259

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 118.36 kDa 
• Atom Count: 8,191 
• Modelled Residue Count: 954 
• Deposited Residue Count: 985 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 reverse transcriptase, p66 subunit	A	557	Human immunodeficiency virus type 1 BH10	Mutation(s): 3  EC: 2.7.7.49
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366  Go to UniProtKB:  P03366

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 reverse transcriptase, p51 subunit	B	428	Human immunodeficiency virus type 1 BH10	Mutation(s): 1  EC: 2.7.7.49
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366  Go to UniProtKB:  P03366

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
T27	C [auth A]	4-{[4-({4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl}amino)pyrimidin-2-yl]amino}benzonitrile C22 H18 N6 YIBOMRUWOWDFLG-ONEGZZNKSA-N
PYZ	CA [auth B], DA [auth B], EA [auth B], FA [auth B], S [auth A], T [auth A]	4-IODOPYRAZOLE C3 H3 I N2 LLNQWPTUJJYTTE-UHFFFAOYSA-N
IOD	AA [auth B], BA [auth B], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], Y [auth B], Z [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
SO4	D [auth A], E [auth A], F [auth A], V [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DMS	GA [auth B], HA [auth B], IA [auth B], JA [auth B], U [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO	G [auth A], H [auth A], W [auth B], X [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
T27	BindingDB:  5CYM	IC50: min: 0.68, max: 84 (nM) from 15 assay(s)
		EC50: min: 0.2, max: 3.6 (nM) from 7 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.229 
• R-Value Work: 0.195 
• R-Value Observed: 0.196 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 162.842	α = 90
b = 73.483	β = 100.67
c = 109.582	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-30 
Deposition Author(s): Bauman, J.D., Arnold, E.

Revision History  

• Version 1.0: 2015-12-30
  Type: Initial release
  
• Version 2.0: 2017-09-27
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2024-03-06
  Changes: Data collection, Database references