6BSJ

Structure of HIV-1 RT complexed with an RNA/DNA hybrid sequence non-preferred for RNA hydrolysis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of HIV-1 reverse transcriptase cleaving RNA in an RNA/DNA hybrid.

Tian, L.Kim, M.S.Li, H.Wang, J.Yang, W.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: 507-512


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
REVERSE TRANSCRIPTASE P66 SUBUNIT
A
558Human immunodeficiency virus type 1 group M subtype BMutation(s): 0 
Gene Names: gag-pol
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P04585
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
REVERSE TRANSCRIPTASE P51 SUBUNIT
B
441Human immunodeficiency virus type 1 group M subtype BMutation(s): 0 
Gene Names: gag-pol
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P04585
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*TP*AP*TP*GP*CP*CP*TP*AP*TP*AP*GP*TP*TP*AP*TP*TP*GP*TP*GP*GP*CP*C)-3')D23Homo sapiens
Entity ID: 4
MoleculeChainsLengthOrganism
RNA (25-MER)R25Homo sapiens
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EFZ
Query on EFZ

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Download CCD File 
A
(-)-6-CHLORO-4-CYCLOPROPYLETHYNYL-4-TRIFLUOROMETHYL-1,4-DIHYDRO-2H-3,1-BENZOXAZIN-2-ONE
DMP-266; Efavirenz
C14 H9 Cl F3 N O2
XPOQHMRABVBWPR-ZDUSSCGKSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
TAM
Query on TAM

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Download CCD File 
R
TRIS(HYDROXYETHYL)AMINOMETHANE
C7 H17 N O3
GKODZWOPPOTFGA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
3DR
Query on 3DR
R
DNA LINKINGC5 H11 O6 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.201 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 163.240α = 90.00
b = 163.240β = 90.00
c = 129.400γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
MOLREPphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States--

Revision History 

  • Version 1.0: 2018-01-03
    Type: Initial release
  • Version 1.1: 2018-01-17
    Type: Author supporting evidence
  • Version 1.2: 2018-04-25
    Type: Data collection, Database references