1N5Y Transferase Immune System Dna date Nov 07, 2002
title Hiv-1 Reverse Transcriptase Crosslinked To Post- Translocation Aztmp-Terminated Dna (Complex P)
authors S.G.Sarafianos, A.D.Clark Jr., K.Das, S.Tuske, J.J.Birktoft, P.Ilankumaran, A.R.Ramesha, J.M.Sayer, D.M.Jerina, P.L.Boyer, S.H.Hughes, E.Arnold
compound source
Molecule: 5'- D(Aptpgpctpapgpgpcpgpcpcpcpgpapapcpapgp Gpgpapcptpgptpg)-3';
Chain: T
Engineered: Yes
Other_details: Dna Template
Synthetic: Yes

Molecule: 5'- D(Acpapgptpcpcpcptpgptptpcpgpgp(Mrg) Pcpgpcpcp(Atm))-3';
Chain: P
Engineered: Yes
Other_details: Dna Primer

Synthetic: Yes

Molecule: Reverse Transcriptase
Chain: A
Synonym: Hiv-1 Rt
Ec: 2.7.7.49
Engineered: Yes
Mutation: Yes
Other_details: P66

Organism_scientific: Human Immunodeficiency Virus 1
Organism_taxid: 11676
Gene: Pol
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Reverse Transcriptase
Chain: B
Synonym: Hiv-1 Rt
Ec: 2.7.7.49
Engineered: Yes
Mutation: Yes
Other_details: P51

Organism_scientific: Human Immunodeficiency Virus 1
Organism_taxid: 11676
Gene: Pol
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Monoclonal Antibody (Light Chain)
Chain: L
Fragment: Fab 28

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090

Molecule: Monoclonal Antibody (Heavy Chain)
Chain: H
Fragment: Fab 28

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
symmetry Space Group: P 32 1 2
R_factor 0.255 R_Free 0.285
crystal
cell
length a length b length c angle alpha angle beta angle gamma
166.700 166.700 221.120 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.10 Å
ligand ATM, MG, MRG enzyme Transferase E.C.2.7.7.49 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


L


Primary referenceStructures of HIV-1 reverse transcriptase with pre- and post-translocation AZTMP-terminated DNA., Sarafianos SG, Clark AD Jr, Das K, Tuske S, Birktoft JJ, Ilankumaran P, Ramesha AR, Sayer JM, Jerina DM, Boyer PL, Hughes SH, Arnold E, EMBO J 2002 Dec 2;21(23):6614-24. PMID:12456667
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (255 Kb) [Save to disk]
  • Biological Unit Coordinates (1n5y.pdb1.gz) 246 Kb
  • LPC: Ligand-Protein Contacts for 1N5Y
  • CSU: Contacts of Structural Units for 1N5Y
  • Likely Quarternary Molecular Structure file(s) for 1N5Y
  • Structure Factors (397 Kb)
  • Retrieve 1N5Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1N5Y from S2C, [Save to disk]
  • Re-refined 1n5y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1N5Y in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 1N5Y
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1N5Y, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1n5ya2, region A:1-429 [Jmol] [rasmolscript] [script source]
        - Domain d1n5ya1, region A:430-558 [Jmol] [rasmolscript] [script source]
        - Domain d1n5yb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1n5yh1, region H:1-123 [Jmol] [rasmolscript] [script source]
        - Domain d1n5yh2, region H:124-225 [Jmol] [rasmolscript] [script source]
        - Domain d1n5yl1, region L:1-107 [Jmol] [rasmolscript] [script source]
        - Domain d1n5yl2, region L:108-211 [Jmol] [rasmolscript] [script source]
  • Fold representative 1n5y from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1n5y_P] [1n5y_A] [1n5y_B] [1n5y_H] [1n5y_L] [1n5y_T] [1n5y]
  • SWISS-PROT database: [P01837] [P03366]
  • Domain organization of [IGKC_MOUSE] [POL_HV1B1] by SWISSPFAM
  • Domains found in 1N5Y: [IG_like] [IGv ] by SMART
  • Other resources with information on 1N5Y
  • Community annotation for 1N5Y at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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