Brand  (β version)

PDB ID: 4IG3

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Ligands
Code Name Style Show Link
DMS Dimethyl sulfoxide PoSSuM
J94 (5s)-6,6-dimethyl-5-[(6r)-8-oxo-6,8-dihydrofuro[3,4-E][1,3]benzodioxol-6-yl]-5,6,7,8-tetrahydro[1,3]dioxolo[4,5-G]isoquinolin-6-ium PoSSuM
T27 4-{[4-({4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl}amino)pyrimidin-2-yl]amino}benzonitrile PoSSuM
Non-standard Residues
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Structure summary

Code : 4IG3   PDBj   RCSB PDB   PDBe
Header : transferase/transferase inhibitor
Title : HIV-1 reverse transcriptase with bound fragment near Knuckles site
Release Data : 2013-02-06
Compound :
mol_id molecule chains synonym
1 Reverse transcriptase/ribonuclease H A EXORIBONUCLEASE H, P66 RT
ec: 2.7.7.49, 2.7.7.7, 3.1.26.13
fragment: P66 (unp residues 600-1154)
mutation: K771A, K772A, C879S
mol_id molecule chains
2 P51 RT B
ec: 2.7.7.49, 2.7.7.7, 3.1.26.13
fragment: P51 (unp residues 600-1027)
mutation: C879S
Source :
mol_id organism_scientific organism_common expression_system
1 Human immunodeficiency virus type 1  (taxid:11678) HIV-1 Escherichia coli  (taxid:511693)
strain: BH10
gene: gag-pol, POL
expression_system_strain: BL21(RIL)
expression_system_vector_type: PLASMID
expression_system_plasmid: PCDF-2
mol_id organism_scientific organism_common expression_system
2 Human immunodeficiency virus type 1 BH10  (taxid:11678) HIV-1 Escherichia coli  (taxid:511693)
strain: BH10
gene: gag-pol, POL
expression_system_strain: BL21(RIL)
expression_system_vector_type: PLASMID
expression_system_plasmid: PCDF-2
Authors : Bauman, J.D., Patel, D., Arnold, E.
Keywords : RNA-DIRECTED DNA POLYMERASE, DNA POLYMERASE, ENDONUCLEASE, HYDROLASE, MULTIFUNCTIONAL ENZYME, transferase-transferase inhibitor complex
Exp. method : X-RAY DIFFRACTION ( 1.950 Å )
Citation :

Detecting Allosteric Sites of HIV-1 Reverse Transcriptase by X-ray Crystallographic Fragment Screening.

Bauman, J.D.,Patel, D.,Dharia, C.  et al.
(2013)  J.Med.Chem.  56 : 2738 - 2746

PubMed: 23342998
DOI: 10.1021/jm301271j

Reaction

Chain : B
UniProt : P03366 (POL_HV1B1)
Reaction: EC: Evidence:
Physiological Direction:
Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro. 3.4.23.16 PROSITE-ProRule:PRU00275
-
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid. 3.1.13.2 ECO:0000250
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[Reverse transcriptase/ribonuclease H]
Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus. 		3.1.26.13 PubMed:2476069
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[Reverse transcriptase/ribonuclease H]
DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate 		2.7.7.49 PROSITE-ProRule:PRU00405, PubMed:2476069
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[Reverse transcriptase/ribonuclease H]
DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate 		2.7.7.7 PROSITE-ProRule:PRU00405, PubMed:2476069
-
Cofactor: Evidence: Note:
Mg(2+) ECO:0000250
Binds 2 magnesium ions for reverse transcriptase polymerase activity.
Mg(2+) ECO:0000250
Binds 2 magnesium ions for ribonuclease H (RNase H) activity. Substrate-binding is a precondition for magnesium binding.
Mg(2+) ECO:0000250
Magnesium ions are required for integrase activity. Binds at least 1, maybe 2 magnesium ions.