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.

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

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

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

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03366
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03366
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
T27 Query on T27 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	4-{[4-({4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl}amino)pyrimidin-2-yl]amino}benzonitrile C₂₂ H₁₈ N₆ YIBOMRUWOWDFLG-ONEGZZNKSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PYZ Query on PYZ Download Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain S [auth A] SDF format, chain CA [auth B] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain T [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain T [auth A]	CA [auth B] DA [auth B] EA [auth B] FA [auth B] S [auth A] 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		Interactions Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain S [auth A] Focus chain T [auth A] Interactions & Density Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain S [auth A] Focus chain T [auth A]
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain J [auth A] SDF format, chain O [auth A] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain O [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B]	AA [auth B] BA [auth B] I [auth A] J [auth A] K [auth A] 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		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain Y [auth B] Focus chain Z [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain V [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A]	D [auth A], E [auth A], F [auth A], V [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain V [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain V [auth B]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain HA [auth B] SDF format, chain IA [auth B] SDF format, chain JA [auth B] SDF format, chain U [auth A] SDF format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain GA [auth B]	GA [auth B], HA [auth B], IA [auth B], JA [auth B], U [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain U [auth A] Interactions & Density Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain U [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B]	G [auth A], H [auth A], W [auth B], X [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain W [auth B] Focus chain X [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
T27	BindingDB: 5CYM	IC50: min: 38, max: 1.00e+4 (nM) from 3 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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-12-30

Deposition Author(s):

Bauman, J.D.

Arnold, E.

Revision History (Full details and data files)

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