6B1S

Hydrogen Bonding Complementary, not size complementarity is key in the formation of the double helix


ChainDomainClassArchitectureTopologyHomology
A3.30.70.270 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits Reverse transcriptase/Diguanylate cyclase domain
A3.30.70.270 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits Reverse transcriptase/Diguanylate cyclase domain
A3.30.70.270 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits Reverse transcriptase/Diguanylate cyclase domain
A3.10.10.10 Alpha Beta Roll HIV Type 1 Reverse Transcriptase Chain A, domain 1
A3.10.10.10 Alpha Beta Roll HIV Type 1 Reverse Transcriptase Chain A, domain 1
B3.30.70.270 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits Reverse transcriptase/Diguanylate cyclase domain
B3.30.70.270 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits Reverse transcriptase/Diguanylate cyclase domain
B3.30.70.270 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits Reverse transcriptase/Diguanylate cyclase domain
B3.10.10.10 Alpha Beta Roll HIV Type 1 Reverse Transcriptase Chain A, domain 1
B3.10.10.10 Alpha Beta Roll HIV Type 1 Reverse Transcriptase Chain A, domain 1

Protein Family Annotation Pfam Database Homepage

ChainsAccessionIdentifierDescriptionCommentsSource
A, BPF02093Gag P30 core shell protein (Gag_p30)Gag P30 core shell protein- Family
A, BPF18697Murine leukemia virus (MLV) integrase (IN) C-terminal domain (MLVIN_C)Murine leukemia virus (MLV) integrase (IN) C-terminal domainThis is the C-terminal domain (CTD) which can be found in murine leukemia virus (MLV) integrase (IN) proteins. The MLV IN C-terminal domain interacts with the bromo and extraterminal (BET) proteins through the ET domain. This interaction provides a s ...This is the C-terminal domain (CTD) which can be found in murine leukemia virus (MLV) integrase (IN) proteins. The MLV IN C-terminal domain interacts with the bromo and extraterminal (BET) proteins through the ET domain. This interaction provides a structural basis for global in vivo integration-site preferences andt disruption of this interaction through truncation mutations affects the global targeting profile of MLV. The CTD consists an SH3 fold followed by a long unstructured tail [1].
Domain
A, BPF01141Gag polyprotein, inner coat protein p12 (Gag_p12)Gag polyprotein, inner coat protein p12- Family
A, BPF01140Matrix protein (MA), p15 (Gag_MA)Matrix protein (MA), p15- Family
A, BPF17919RNase H-like domain found in reverse transcriptase (RT_RNaseH_2)RNase H-like domain found in reverse transcriptase- Domain
A, BPF00075RNase H (RNase_H)RNase HRNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers.Domain
A, BPF00098Zinc knuckle (zf-CCHC)Zinc knuckleThe zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eu ...The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.
Domain
A, BPF00077Retroviral aspartyl protease (RVP)Retroviral aspartyl proteaseSingle domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a ...Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases such as pepsins, cathepsins, and renins (Pfam:PF00026).
Domain
A, BPF16721Zinc-finger like, probable DNA-binding (zf-H3C2)Zinc-finger like, probable DNA-bindingThis is a family of probably DNA-binding zinc-fingers found on Gag-Pol polyproteins from mouse retroviruses. Added to clan to resolve overlaps with zf-H2C2, but neither are true members.Domain
A, BPF00078Reverse transcriptase (RNA-dependent DNA polymerase) (RVT_1)Reverse transcriptase (RNA-dependent DNA polymerase)- Family
A, BPF00665Integrase core domain (rve)Integrase core domainIntegrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain Pfam:PF02022. This domain is the central catalytic domain. The ca ...Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain Pfam:PF02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain Pfam:PF00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyses the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site [1].
Domain

Gene Product Annotation Gene Product Annotation

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, BReverse transcriptase
E, FDNA (5'-D(*CP*TP*TP*AP*TP*AP*(CGY)P*(CGY)P*TP*TP*TP*AP*TP*AP*AP*G)-3')none none none