Biological Assembly 1  

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 114419.02 
• Atom Count: 7814 
• Residue Count: 983 
• Unique protein chains: 2

1FKP

CRYSTAL STRUCTURE OF NNRTI RESISTANT K103N MUTANT HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH NEVIRAPINE

• DOI: 10.2210/pdb1FKP/pdb

• Classification: TRANSFERASE
• Organism(s): Human immunodeficiency virus type 1 group M subtype B
• Expression System: Escherichia coli
• Mutation(s): 2 


• Deposited: 2000-08-10 Released: 2000-11-03 
• Deposition Author(s): Ren, J., Milton, J., Weaver, K.L., Short, S.A., Stuart, D.I., Stammers, D.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.281 
• R-Value Work: 0.215 

Literature

Structural basis for the resilience of efavirenz (DMP-266) to drug resistance mutations in HIV-1 reverse transcriptase.

Ren, J., Milton, J., Weaver, K.L., Short, S.A., Stuart, D.I., Stammers, D.K.

(2000) Structure Fold.Des. 8: 1089-1094

• PubMed: 11080630 
• Primary Citation of Related Structures:  
  1FKO, 1FK9


• PubMed Abstract: 
  

Efavirenz is a second-generation non-nucleoside inhibitor of HIV-1 reverse transcriptase (RT) that has recently been approved for use against HIV-1 infection. Compared with first-generation drugs such as nevirapine, efavirenz shows greater resilience to drug resistance mutations within HIV-1 RT. In order to understand the basis for this resilience at the molecular level and to help the design of further-improved anti-AIDS drugs, we have determined crystal structures of efavirenz and nevirapine with wild-type RT and the clinically important K103N mutant.

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Related Citations: 

• Design of MKC-442 (emivirine) analogues with improved activity against drug-resistant HIV mutants
  Hopkins, A.L.,Ren, J.,Tanaka, H.,Baba, M.,Okamato, M.,Stuart, D.I.,Stammers, D.K.
  (1999) J.Med.Chem. 42: 4500
• Mechanism of Inhibition of HIV-1 Reverse Transcriptase by Non-nucleoside Inhibitors
  Esnouf, R.M.,Ren, J.,Ross, C.K.,Jones, E.Y.,Stammers, D.K.,Stuart, D.I.
  (1995) Nat.Struct.Mol.Biol. 2: 303
• Continuous and discontinuous changes in the unit cell of HIV-1 reverse transcriptase crystals on dehydration
  Esnouf, R.M.,Ren, J.,Garman, E.,Somers, D.O.,Ross, C.K.,Jones, E.Y.,K Stammers, D.,Stuart, D.I.
  (1998) Acta Crystallogr.,Sect.D 54: 938
• Complexes of HIV-1 reverse transcriptase with inhibitors of the HEPT series reveal conformational changes relevant to the design of potent non-nucleoside inhibitors
  L Hopkins, A.,Ren, J.,Esnouf, R.M.,Willcox, B.E.,Jones, E.Y.,Ross, C.K.,Miyasaka, T.,Walker, R.T.,Tanaka, H.,Stammers, D.K.,Stuart, D.I.
  (1996) J.Med.Chem. 39: 1589
• 3'-azido-3'-deoxythymidine drug resistance mutations in HIV-1 reverse transcriptase can induce long range conformational changes
  Ren, J.,Esnouf, R.M.,Hopkins, A.L.,Jones, E.Y.,Kirby, I.,Keeling, J.,Ross, C.K.,Larder, B.A.,Stuart, D.I.,Stammers, D.K.
  (1998) Proc.Natl.Acad.Sci.USA 95: 9518
• Crystals of HIV-1 Reverse Transcriptase Diffracting to 2.2 Angstrom Resolution
  Stammers, D.K.,Somers, D.O.,Ross, C.K.,Kirby, I.,Ray, P.H.,Wilson, J.E.,Norman, M.,Ren, J.,Esnouf, R.M.,Garman, E.,Jones, E.Y.,Stuart, D.I.
  (1994) J.Mol.Biol. 242: 586
• Binding of the second generattion non-nucleoside inhibitor S-1153 to HIV-1 reverse transcriptase involves extensive main chain hydrogen bonding
  Ren, J.,Nichols, C.,Bird, L.E.,Fujiwara, T.,Suginoto, H.,Stuart, D.I.,Stammers, D.K.
  (2000) J.Biol.Chem. 275: 14316
• Phenethylthiazolylthiourea (PETT) non-nucleoside inhibitors of HIV-1 and HIV-2 reverse transcriptases: structural and biochemical analyses
  Ren, J.,Diprose, J.,Warren, J.,Esnouf, R.M.,Bird, L.E.,Ikemizu, S.,Slater, M.,Milton, J.,Balzarini, J.,Stuart, D.I.,Stammers, D.K.
  (2000) J.Biol.Chem. 275: 5633
• The structure of HIV-1 reverse transcriptase complexed with 9-chloro-TIBO: lessons for inhibitor design
  Ren, J.,Esnouf, R.M.,Hopkins, A.L.,Ross, C.K.,Jones, E.Y.,Stammers, D.K.,Stuart, D.I.
  (1995) Structure 3: 915
• Crystallographic analysis of the binding modes of non-nucleoside thiazoloisoindolinone inhibitors to HIV-1 reverse transcriptase and comparison with modeling studies
  Ren, J.,Esnouf, R.M.,Hopkins, A.L.,Stuart, D.I.,Stammers, D.K.
  (1999) J.Med.Chem. 42: 3845
• Unique features in the structure of the complex between HIV-1 reverse transcriptase and the bis(heteroaryl)piperazine (BHAP) U-90152 explain resistance mutations for this non-nucleoside inhibitor
  Esnouf, R.M.,Ren, J.,Hopkins, A.L.,Ross, C.K.,Jones, E.Y.,Stammers, D.K.,Stuart, D.I.
  (1997) Proc.Natl.Acad.Sci.USA 94: 3984
• Crystal structures of reverse transcriptase in complex with carboxanilide derivatives
  Ren, J.,Esnouf, R.M.,Hopkins, A.L.,Warren, J.,Balzarini, J.,Stuart, D.I.,Stammers, D.K.
  (1998) Biochemistry 37: 14394
• High Resolution Structures of HIV-1 RT From Four RT-inhibitor Complexes
  Ren, J.,Esnouf, R.M.,Garman, E.,Somers, D.O.,Ross, C.K.,Kirby, I.,Keeling, J.,Darby, G.,Jones, E.Y.,Stuart, D.I.,Stammers, D.K.
  (1995) Nat.Struct.Mol.Biol. 2: 293




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Organizational Affiliation: 

Structural Biology Division The Wellcome Trust Centre for Human Genetics University of Oxford OX3 7BN, Oxford, United Kingdom.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
HIV-1 RT, A-CHAIN	A	543	Human immunodeficiency virus type 1 group M subtype B	Mutation(s): 1  Gene Names: gag-pol
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B) Go to UniProtKB:  P04585

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
HIV-1 RT, B-CHAIN	B	440	Human immunodeficiency virus type 1 group M subtype B	Mutation(s): 1  Gene Names: gag-pol
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B) Go to UniProtKB:  P04585

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NVP	A	11-CYCLOPROPYL-5,11-DIHYDRO-4-METHYL-6H-DIPYRIDO[3,2-B:2',3'-E][1,4]DIAZEPIN-6-ONE NON-NUCLEOSIDE RT INHIBITOR NEVIRAPINE C15 H14 N4 O NQDJXKOVJZTUJA-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.281 
• R-Value Work: 0.215 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 139.700	α = 90.00
b = 109.800	β = 90.00
c = 72.900	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-08-10 
• Released Date: 2000-11-03 
• Deposition Author(s): Ren, J., Milton, J., Weaver, K.L., Short, S.A., Stuart, D.I., Stammers, D.K.

Revision History 

• Version 1.0: 2000-11-03
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2018-01-24
  Type: Database references
• Version 1.4: 2018-01-31
  Type: Database references
• Version 1.5: 2018-03-14
  Type: Database references