3KLE

Crystal structure of AZT-resistant HIV-1 Reverse Transcriptase crosslinked to a DSDNA with a bound excision product, AZTPPPPA

• PDB DOI: https://doi.org/10.2210/pdb3KLE/pdb
• NAKB: 3KLE

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


• Deposited: 2009-11-07 Released: 2010-09-22 
• Deposition Author(s): Tu, X., Das, K., Sarafianos, S.G., Arnold, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.308 
• R-Value Work: 0.280 
• R-Value Observed: 0.280 

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 526.9 kDa 
• Atom Count: 36,120 
• Modelled Residue Count: 4,106 
• Deposited Residue Count: 4,188 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse transcriptase/ribonuclease H	A, C [auth E], E [auth I], G [auth M]	562	Human immunodeficiency virus type 1 BH10	Mutation(s): 7  Gene Names: gag-pol EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.4 (PDB Primary Data)
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
p51 RT	B, D [auth F], F [auth J], H [auth N]	437	Human immunodeficiency virus type 1 BH10	Mutation(s): 1  Gene Names: gag-pol
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366  Go to UniProtKB:  P03366

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (25-MER)	I [auth C], K [auth G], M [auth K], O	27	N/A

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(2DA))-3')	J [auth D], L [auth H], N [auth L], P	21	N/A

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-fructofuranose-(2-1)-alpha-D-glucopyranose	Q	2		N/A
Glycosylation Resources
GlyTouCan:  G49187ZK GlyCosmos:  G49187ZK

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZP4	BA [auth I], EA [auth M], T [auth A], X [auth E]	[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl] [(2S,3S,5R)-3-azido-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl hydrogen phosphate C20 H28 N10 O19 P4 NHJROJSMKQZWCP-SLFMBYJQSA-N
GOL	U [auth B], Y [auth F]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	AA [auth I], CA [auth M], DA [auth M], R [auth A], S [auth A], V [auth E], W [auth E], Z [auth I]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900032	Q	surcrose isoform	Oligosaccharide / Substrate analog

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.308 
• R-Value Work: 0.280 
• R-Value Observed: 0.280 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.738	α = 90
b = 283.33	β = 89.73
c = 155.233	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-22 
Deposition Author(s): Tu, X., Das, K., Sarafianos, S.G., Arnold, E.

Revision History  

• Version 1.0: 2010-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2021-10-13
  Changes: Database references, Structure summary